search

nf-core / configs

Config files used to define parameters specific to compute environments at different Institutions
https://nf-co.re/configs
MIT License
85 stars 264 forks source link

Fix `nextflow config -show-profiles` command #162

Closed ewels closed 2 years ago

ewels commented 4 years ago

This code block breaks the functionality of nextflow config -show-profiles with all nf-core pipelines:

https://github.com/nf-core/configs/blob/bb7f67e2b556e1deda34b51799d654603d9c8c9f/conf/bi.config#L10-L18

Gives:

$ nextflow config -a nf-core/rnaseq
ERROR: Environment variable NXF_GLOBAL_CONFIG is missing. Set it to point to global.config file.
WARNING: Could not load nf-core/config profiles: https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config
No such file: Config file does not exist: https://raw.githubusercontent.com/nf-core/configs/master/conf/conf/test.config

I thought that this was a nextflow bug at first, see https://github.com/nextflow-io/nextflow/issues/1639

@apeltzer - what's going on in this code? Can we refactor it somehow?

apeltzer commented 4 years ago

@piotr-faba-ardigen - can we chat about this ?

piotr-faba-ardigen commented 4 years ago

Thanks for letting me know. I didn't test this scenario. I will check how I can modify this no to break this.

apeltzer commented 4 years ago

Just to provide some more clarity on this: We use this config to run all nf-core pipelines internally at BI, but don't want / can't disclose the URL to our own managed central config repository publicly.

This way worked quite nicely without breaking the way we import configs in nf-core, so we thought it would be fine, given that the config will just work from within here with someone having the ENV variable set appropriately. I wondered in the beginning whether it will break things in the central configs repository (which it doesn't - just provides a proper error if its not set), but seemingly there is a side effect on the function you posted above @ewels 😞

ewels commented 4 years ago

Yeah, I guess it happens whenever that config file is parsed. Usually that's only when loading the profile, but in this case we are trying to list all profiles and it gets executed.

Could you just tweak it to throw a warning instead of halting all execution with an exception? Or better still, if you have static hostnames, could you check that before running the function?

piotr-faba-ardigen commented 4 years ago

FYI, I verified one more thing. I run the command nextflow config -show-profiles pointing at configs at this commit which is before my addition. In this case another error from the prince.config profile is thrown.

[faba@xxx sarek]$ nextflow config -show-profiles
Unknown config attribute `profiles.prince.SCRATCH` -- check config file: /home/faba/nf-core/sarek/nextflow.config

So there may be more fixes to do, before it works. Probably a good follow up would be to add nextflow config -show-profiles command to CI as another test. Otherwise this may get broken again in the future.

apeltzer commented 4 years ago

The PRINCE config also has a custom variable set - so similar issue there and would need a fix too ;-)

apeltzer commented 4 years ago

I think your fix looks good - if you want to add a CI test yourself that would be cool, otherwise I can do it too.

ewels commented 4 years ago

Reopening this issue and renaming it, just to keep it here until nextflow config -show-profiles works...

ewels commented 4 years ago

Note that when I run in the nf-core/configs root directory I get an different to the profiles.prince.SCRATCH one above:

$ nextflow config -show-profiles .
No such file: Config file does not exist: /Users/philewels/GitHub/nf-core/configs/[:]/conf/awsbatch.config

Any ideas?

Phil

piotr-faba-ardigen commented 4 years ago

It's because prince profile uses also a ENV VAR which if undefined breaks things. An if statement verifying if it's set should be added in it, like in bi.config. I noticed that missing ENV VAR is often substituted with [:] by Groovy/Nextflow.

ewels commented 4 years ago

I'm not quite sure that's right. It was a problem with the BI config because the code was throwing an Exception, which halted everything. Missing env vars throw a warning but that's it I think.

After playing a bit, I think it's because when I run nextflow config in the configs directory, it uses the nextflow.config which is used basically nowhere. With this file, params.cusom_config_base is not set, so all of the includeConfig statements fail when they try to load the profile config files. Adding this to nextflow.config solves the problem.

I've made a PR in #165 to fix this.

ewels commented 4 years ago

Ok, so running nextflow config -show-profiles in the configs root now gives me this:

``` params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } profiles { awsbatch { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'awsbatch' queue = false } aws { region = 'eu-west-1' } executor { awscli = '/home/ec2-user/miniconda/bin/aws' } } bi { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } } bigpurple { singularityDir = '/gpfs/scratch/philewels/singularity_images_nextflow' params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true autoMounts = true cacheDir = '/gpfs/scratch/philewels/singularity_images_nextflow' } process { beforeScript = '\nmodule load singularity/3.1\nmodule load squashfs-tools/4.3\n' executor = 'slurm' } } binac { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true envWhitelist = 'TZ' } process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'pbs' queue = Script8D41799E9EBC324A05706CF8BF7B6705$_run_closure3$_closure6@1252b961 } weblog { enabled = true url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows' } } cbe { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'slurm' queue = Script826B914DFFB3C198A0EEA92D9BBF2394$_run_closure2$_closure5@9ed238c clusterOptions = Script826B914DFFB3C198A0EEA92D9BBF2394$_run_closure2$_closure6@56276db8 } singularity { enabled = true cacheDir = '/resources/containers' } } ccga_dx { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true runOptions = '-B /mnt' } executor { queueSize = 100 } process { executor = 'slurm' queue = 'htc' } } ccga_med { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true runOptions = '-B /work_ifs -B /scratch' cacheDir = '/work_ifs/ikmb_repository/singularity_cache/' } executor { queueSize = 100 } process { executor = 'slurm' queue = 'all' } } cfc { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true cacheDir = '/nfsmounts/container' } process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'slurm' queue = ScriptEFFA82B66F0E9C33C6DAB888F9583FCB$_run_closure3$_closure6@51e8e6e6 scratch = 'true' } weblog { enabled = true url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows' } } cfc_dev { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true } process { beforeScript = 'module load devel/singularity/3.4.2' executor = 'slurm' queue = ScriptE9805C9E38B950D7C1D5F64B7567BA92$_run_closure3$_closure6@56f6d40b scratch = 'true' } weblog { enabled = true url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows' } } crick { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true autoMounts = true } process { beforeScript = 'module load Singularity/2.6.0-foss-2016b' executor = 'slurm' } } czbiohub_aws { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } docker { enabled = true } process { executor = 'awsbatch' queue = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036' errorStrategy = 'ignore' } workDir = 's3://czb-nextflow/intermediates/' aws { region = 'us-west-2' } executor { awscli = '/home/ec2-user/miniconda/bin/aws' } profiles { } } highpriority { process { executor = 'awsbatch' queue = 'highpriority-971039e0-830c-11e9-9e0b-02c5b84a8036' errorStrategy = 'ignore' } } ebc { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } cleanup = true conda { cacheDir = '/ebc_data/nf-core/conda' } process { executor = 'slurm' conda = '/Users/philewels/GitHub/nf-core/configs/environment.yml' beforeScript = 'module load nextflow' } executor { queueSize = 16 } } icr_davros { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true autoMounts = true } executor { submitRateLimit = '2 sec' } process { executor = 'LSF' } } genotoul { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true runOptions = '-B /bank -B /work2 -B /work -B /save -B /home' } process { executor = 'slurm' } } google { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'google-lifesciences' errorStrategy = ScriptA3CBBCA2F8617505A4865505EBBADC5D$_run_closure2@36676c1a maxRetries = 5 } zone = 'europe-west2-c' lifeSciences { debug = false preemptible = true } workDir = false } denbi_qbic { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true } process { executor = 'pbs' queue = Script9E8184524F176DFF883162C658DFEC73$_run_closure3$_closure6@5b408dc3 } weblog { enabled = true url = 'https://services.qbic.uni-tuebingen.de/flowstore/workflows' } } genouest { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true autoMounts = true runOptions = '-B /scratch:/scratch -B /local:/local -B /db:/db' } process { executor = 'slurm' } } gis { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'sge' clusterOptions = ScriptC6B693C4EFEBAF672C169A8D81A9AC54$_run_closure2$_closure4@4d098f9b penv = 'OpenMP' errorStrategy = ScriptC6B693C4EFEBAF672C169A8D81A9AC54$_run_closure2$_closure5@2dbf4cbd beforeScript = ScriptC6B693C4EFEBAF672C169A8D81A9AC54$_run_closure2$_closure6@20b5f2ac } } hebbe { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true } process { executor = 'slurm' clusterOptions = Script2CA8F8F751980B48A218709120424BE8$_run_closure3$_closure5@7fc44dec withName:'*' { memory = null } } } kraken { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'local' } docker { enabled = true mountFlags = 'z' fixOwnership = true } } munin { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } process { executor = 'local' maxForks = 46 } singularity { enabled = true cacheDir = '/data1/containers/' } docker { enabled = false mountFlags = 'z' fixOwnership = true } } pasteur { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true autoMounts = true runOptions = '-B /local/scratch:/tmp' } process { executor = 'slurm' } } phoenix { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true envWhitelist = 'SINGULARITY_BINDPATH' autoMounts = true } process { beforeScript = 'module load Singularity/2.5.2-GCC-5.4.0-2.26' executor = 'slurm' } } prince { singularityDir = '$SCRATCH/singularity_images_nextflow' singularityModule = 'singularity/3.2.1' squashfsModule = 'squashfs/4.3' params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true cacheDir = '$SCRATCH/singularity_images_nextflow' } process { beforeScript = 'module load singularity/3.2.1 squashfs/4.3' executor = 'slurm' } } shh { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } cleanup = true singularity { enabled = true autoMounts = true runOptions = '-B /run/shm:/run/shm' cacheDir = '/projects1/singularity_scratch/cache/' } process { executor = 'slurm' queue = ScriptD3A063E44EFB34480121EB28DB694474$_run_closure3$_closure6@7e3060d8 } executor { queueSize = 16 } profiles { } } cdag { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } } sdag { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } } uct_hpc { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true cacheDir = '/bb/DB/bio/singularity-containers/' autoMounts = true } process { executor = 'slurm' queue = 'ada' maxRetries = 4 clusterOptions = '--account cbio' stageInMode = 'symlink' stageOutMode = 'rsync' } executor { queueSize = 15 } } uppmax { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true } process { executor = 'slurm' clusterOptions = Script69AF3EAA68DC7599AA0EEF12A9BF86BB$_run_closure3$_closure6@293d0107 queue = 'devel' } profiles { } } devel { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } executor { queueSize = 1 } } utd_ganymede { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true envWhitelist = 'SINGULARITY_BINDPATH' autoMounts = true } process { beforeScript = 'module load singularity/2.4.5' executor = 'slurm' queue = 'genomics' } } uzh { params { custom_config_base = '.' config_profile_description = 'UZH science cloud profile provided by nf-core/configs' config_profile_contact = 'Judith Neukamm/Alexander Peltzer (@JudithNeukamm, @apeltzer)' config_profile_url = 'https://www.id.uzh.ch/en/scienceit/infrastructure/sciencecloud.html' awsqueue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036' awsregion = 'us-west-2' awscli = '/home/ec2-user/miniconda/bin/aws' tracedir = './' globalConfig = null igenomes_base = '/sw/data/uppnex/igenomes/' max_memory = '1.8 TB' max_cpus = 112 max_time = '7d' saveReference = true seq_center = 'czbiohub' seqCenter = 'czbiohub' gencode_base = 's3://czbiohub-reference/gencode' transgenes_base = 's3://czbiohub-reference/transgenes' refseq_base = 's3://czbiohub-reference/ncbi/genomes/refseq/' igenomes_ignore = true igenomesIgnore = true fc_extra_attributes = 'gene_name' fc_group_features = 'gene_id' fc_group_features_type = 'gene_type' trim_pattern = '_+S\\d+' genomes { GRCh38 { fasta = 's3://czbiohub-reference/gencode/human/v30/GRCh38.p12.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/human/v30/gencode.v30.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/human/v30/STARIndex/' salmon_index = 's3://czbiohub-reference/gencode/human/v30/salmon_index/' } GRCm38 { fasta = 's3://czbiohub-reference/gencode/mouse/vM21/GRCm38.p6.genome.ERCC92.fa' gtf = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.annotation.ERCC92.gtf' transcript_fasta = 's3://czbiohub-reference/gencode/mouse/vM21/gencode.vM21.transcripts.ERCC92.fa' star = 's3://czbiohub-reference/gencode/mouse/vM21/STARIndex/' } 'AaegL5.0' { fasta = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.fna' gtf = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.gtf' bed = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/GCF_002204515.2_AaegL5.0_genomic.bed' star = 's3://czbiohub-reference/ncbi/genomes/refseq//invertebrate/Aedes_aegypti/GCF_002204515.2_AaegL5.0/nf-core--rnaseq/reference_genome/star/' } } transgenes { ChR2 { fasta = 's3://czbiohub-reference/transgenes/ChR2/ChR2.fa' gtf = 's3://czbiohub-reference/transgenes/ChR2/ChR2.gtf' } Cre { fasta = 's3://czbiohub-reference/transgenes/Cre/Cre.fa' gtf = 's3://czbiohub-reference/transgenes/Cre/Cre.gtf' } ERCC { fasta = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.fa' gtf = 's3://czbiohub-reference/transgenes/ERCC92/ERCC92.gtf' } GCaMP6m { fasta = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.fa' gtf = 's3://czbiohub-reference/transgenes/GCaMP6m/GCaMP6m.gtf' } GFP { fasta = 's3://czbiohub-reference/transgenes/Gfp/Gfp.fa' gtf = 's3://czbiohub-reference/transgenes/Gfp/Gfp.gtf' } NpHR { fasta = 's3://czbiohub-reference/transgenes/NpHR/NpHR.fa' gtf = 's3://czbiohub-reference/transgenes/NpHR/NpHR.gtf' } RCaMP { fasta = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.fa' gtf = 's3://czbiohub-reference/transgenes/RCaMP/RCaMP.gtf' } RGECO { fasta = 's3://czbiohub-reference/transgenes/RGECO/RGECO.fa' gtf = 's3://czbiohub-reference/transgenes/RGECO/RGECO.gtf' } Tdtom { fasta = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.fa' gtf = 's3://czbiohub-reference/transgenes/Tdtom/Tdtom.gtf' } 'Car-T' { fasta = 's3://czbiohub-reference/transgenes/car-t/car-t.fa' gtf = 's3://czbiohub-reference/transgenes/car-t/car-t.gtf' } zsGreen { fasta = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.fa' gtf = 's3://czbiohub-reference/transgenes/zsGreen/zsGreen.gtf' } } cpus = 10 save_reference = true google_zone = 'europe-west2-c' google_bucket = false google_debug = false google_preemptible = true config_profile_name = 'KRAKEN' singularity_cache_dir = '/bb/DB/bio/singularity-containers/' hpc_queue = 'ada' hpc_account = '--account cbio' genome = 'GRCh37' hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']] } singularity { enabled = true } process { executor = 'slurm' } } } WARN: Unknown config attribute `profiles.prince.SCRATCH` -- check config file: /Users/philewels/GitHub/nf-core/configs/nextflow.config ```

That's all to STDOUT. The log warning from the BI config comes to STDERR as expected:

WARNING: For bi.config requires NXF_GLOBAL_CONFIG env var to be set. Point it to global.config file if you want to use this profile.

Buried at the bottom of that big config dump is the prince config SCRATCH warning from Nextflow:

WARN: Unknown config attribute `profiles.prince.SCRATCH` -- check config file: /Users/philewels/GitHub/nf-core/configs/nextflow.config
ewels commented 4 years ago

Updated the Prince config to do the same thing as the BI config. Now both warnings come to STDERR. I also added CI checks for this. Should be good now I think!

apeltzer commented 2 years ago

Should be fixed now in #165