Open ewels opened 3 years ago
Checking which assets currently available in iGenomes have corresponding recipes available in refgenie. https://github.com/refgenie/refgenie/blob/master/refgenie/asset_build_packages.py
readme
, mito_name
and macs_gsize
are all specific assets that would have to be added manually, as long as that is allowed by refgenie. For bed12
we should be able to write a build recipe and add it to the asset_build_packages.py
@KevinMenden, I can help put together the refgenie asset recipes for the missing asset types. Where can I find commands used to create these?
Needs more data than that for Sarek (cf: https://github.com/nf-core/sarek/blob/05194ed421d7fef6b7cef05fe267a95d8ceb4d6c/conf/igenomes.config#L36-L57)
TODO:
Still to add:
These can be added as attributes to eg. the Fast file rather than dedicated uploads:
Readme can probably be skipped, as RefGenie hopefully already has enough provenance for assets.
Split from #592, related directly to #1084
We want to transition away from using AWS-iGenomes to using the central RefGenie server(s) to host reference genome assets for the nf-core pipelines. To do this, we need to make sure that everything we currently have is available on a AWS refgenie server somewhere. Once all assets are mirrored we can do a clean swap in the config.
Going from
igenomes.config
, here is a check-list:Summary of genomes
* [ ] GRCh37 * [ ] GRCh38 * [ ] GRCm38 * [ ] TAIR10 * [ ] EB2 * [ ] UMD3.1 * [ ] WBcel235 * [ ] CanFam3.1 * [ ] GRCz10 * [ ] BDGP6 * [ ] EquCab2 * [ ] EB1 * [ ] Galgal4 * [ ] Gm01 * [ ] Mmul_1 * [ ] IRGSP-1.0 * [ ] CHIMP2.1.4 * [ ] Rnor_6.0 * [ ] R64-1-1 * [ ] EF2 * [ ] Sbi1 * [ ] Sscrofa10.2 * [ ] AGPv3 * [ ] hg38 * [ ] hg19 * [ ] mm10 * [ ] bosTau8 * [ ] ce10 * [ ] canFam3 * [ ] danRer10 * [ ] dm6 * [ ] equCab2 * [ ] galGal4 * [ ] panTro4 * [ ] rn6 * [ ] sacCer3 * [ ] susScr3Detailed version with asset types
* [ ] GRCh37 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] GRCh38 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] GRCm38 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] TAIR10 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] EB2 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] UMD3.1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] WBcel235 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] CanFam3.1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] GRCz10 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] BDGP6 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] EquCab2 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] EB1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] Galgal4 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] Gm01 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] Mmul_1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] IRGSP-1.0 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] CHIMP2.1.4 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] Rnor_6.0 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] R64-1-1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] EF2 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] Sbi1 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] Sscrofa10.2 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] AGPv3 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] hg38 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] hg19 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] mm10 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] blacklist * [ ] bosTau8 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] ce10 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] canFam3 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] danRer10 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] dm6 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] macs_gsize * [ ] equCab2 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] galGal4 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] panTro4 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_name * [ ] rn6 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] mito_name * [ ] sacCer3 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] readme * [ ] mito_name * [ ] macs_gsize * [ ] susScr3 * [ ] fasta * [ ] bwa * [ ] bowtie2 * [ ] star * [ ] bismark * [ ] gtf * [ ] bed12 * [ ] readme * [ ] mito_nameFrom @nsheff:
See also: