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WarrenLab / hic-scaffolding-nf

Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
MIT License
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More hic files #1

Closed ardy20 closed 1 year ago

ardy20 commented 1 year ago

Hello Thanks for creating this pipeline. I am trying to use it in our HPC cluster but I have a few questions.

How to change the script if we have more hic data (let's say 4 or more)? For -profile conda option, should we use it once (to install tools) or every time we run the pipeline? What should be the queue's name in .config file? Do I need to obtain it from our system admin? Regards

ardy20 commented 1 year ago

Hello Again

It looks that workflow stopped working with the following messages.

I run the script as:

nextflow run WarrenLab/hic-scaffolding-nf -profile conda --juicer-tools-jar /scratch/project/hic-scaffolding-nf/juicer_tools_1.22.01.jar --contigs OAust.hic.primary_ctg.fa --r1Reads o.austral.01.fastq --r2Reads o.austral.02.fastq

N E X T F L O W ~ version 22.10.1 Pulling WarrenLab/hic-scaffolding-nf ... downloaded from https://github.com/WarrenLab/hic-scaffolding-nf.git Launching https://github.com/WarrenLab/hic-scaffolding-nf [distraught_goldberg] DSL2 - revision: 2a562a38da [main]

[- ] process > PRINT_VERSIONS - executor > local (4) [- ] process > PRINT_VERSIONS - executor > local (4) [6a/6748c5] process > PRINT_VERSIONS [100%] 1 of 1 ✔ [10/f22e9f] process > SAMTOOLS_FAIDX (1) [100%] 1 of 1 ✔ [c9/a70b7a] process > CHROMAP_INDEX (1) [100%] 1 of 1 ✔ [97/097af0] process > CHROMAP_ALIGN (1) [ 0%] 0 of 1 [- ] process > YAHS_SCAFFOLD - [- ] process > JUICER_PRE - [- ] process > ASSEMBLY_STATS -

esrice commented 1 year ago

How to change the script if we have more hic data (let's say 4 or more)?

The simplest way to do this is probably to cat all the r1s and r2s together respectively.

For -profile conda option, should we use it once (to install tools) or every time we run the pipeline?

Every time, so that it loads the conda env it created the first time.

What should be the queue's name in .config file? Do I need to obtain it from our system admin?

This depends on what batch system you are using, if any. See nextflow docs and talk to your system admin, yes

esrice commented 1 year ago

Hello Again

It looks that workflow stopped working with the following messages.

I run the script as:

nextflow run WarrenLab/hic-scaffolding-nf -profile conda --juicer-tools-jar /scratch/project/hic-scaffolding-nf/juicer_tools_1.22.01.jar --contigs OAust.hic.primary_ctg.fa --r1Reads o.austral.01.fastq --r2Reads o.austral.02.fastq

N E X T F L O W ~ version 22.10.1 Pulling WarrenLab/hic-scaffolding-nf ... downloaded from https://github.com/WarrenLab/hic-scaffolding-nf.git Launching https://github.com/WarrenLab/hic-scaffolding-nf [distraught_goldberg] DSL2 - revision: 2a562a3 [main]

[- ] process > PRINT_VERSIONS - executor > local (4) [- ] process > PRINT_VERSIONS - executor > local (4) [6a/6748c5] process > PRINT_VERSIONS [100%] 1 of 1 ✔ [10/f22e9f] process > SAMTOOLS_FAIDX (1) [100%] 1 of 1 ✔ [c9/a70b7a] process > CHROMAP_INDEX (1) [100%] 1 of 1 ✔ [97/097af0] process > CHROMAP_ALIGN (1) [ 0%] 0 of 1 [- ] process > YAHS_SCAFFOLD - [- ] process > JUICER_PRE - [- ] process > ASSEMBLY_STATS -

I don't see any error message here; either this is still running just fine or you didn't copy the full output.

ardy20 commented 1 year ago

Hello Thanks. The pipeline worked perfectly. I am checking the results now,