Switch sarek to DSL 2 - Githubissues

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

https://nf-co.re/sarek

MIT License

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Switch sarek to DSL 2 #132

Closed maxulysse closed 3 years ago

grst commented 4 years ago

List of modules being ported for the chipseq pipeline: https://github.com/nf-core/chipseq/issues/167

maxulysse commented 4 years ago

we opened a new branch to work on dsl2: https://github.com/nf-core/sarek/tree/dsl2

FriederikeHanssen commented 4 years ago

[ ] conda-forge::markdown=3.1.1
[ ] conda-forge::pymdown-extensions=6.0
[ ] conda-forge::pygments=2.5.2
[ ] bioconda::ascat=2.5.2
[ ] bioconda::bcftools=1.9
[ ] bioconda::bwa=0.7.17, Use BWA Mem2 in the future here
[ ] bioconda::cancerit-allelecount=4.0.2
[ ] bioconda::cnvkit=0.9.6
[ ] bioconda::control-freec=11.5
[ ] bioconda::ensembl-vep=99.2
[ ] bioconda::fastqc=0.11.9
[ ] bioconda::freebayes=1.3.2
[ ] bioconda::gatk4-spark=4.1.7.0
[ ] bioconda::genesplicer=1.0
[ ] bioconda::htslib=1.9
[ ] bioconda::manta=1.6.0
[ ] bioconda::msisensor=0.5
[ ] bioconda::multiqc=1.8
[ ] bioconda::qualimap=2.2.2d
[x] bioconda::samtools=1.9
[ ] bioconda::snpeff=4.3.1t
[ ] bioconda::strelka=2.9.10
[ ] bioconda::tiddit=2.7.1
[ ] bioconda::trim-galore=0.6.5
[ ] bioconda::vcfanno=0.3.2
[ ] bioconda::vcftools=0.1.16
[ ] conda-forge::pigz=2.3.4
[ ] conda-forge::r-ggplot2=3.3.0

FriederikeHanssen commented 4 years ago

Just added all the tools from the environment yaml of release 2.6.1 with their versions, so we can now port as is.

maxulysse commented 4 years ago

Or you can already port https://github.com/nf-core/sarek/issues/228

FriederikeHanssen commented 4 years ago

Ticked the modules that are already in modules repo and have the same version.

modules that are in repo, but different version:

[x] FastQC - 0.11.8
[x] Trim Galore - 0.6.4

FriederikeHanssen commented 4 years ago

[x] Add subworkflow for indices (Rike)
[x] Add modules for indices (Rike)

FriederikeHanssen commented 4 years ago

Here some more comments to address:

https://github.com/nf-core/modules/pull/50

FriederikeHanssen commented 4 years ago

We should probably double check at some point that all the tmp directories are set properly, so that they work, when the users changes it i.e. to scratch=/my-favorite-dir , e.g. here: https://github.com/nf-core/sarek/blob/a7679b9b5c178351b1e96a3ffe7ee81ddf9aad06/conf/modules.config#L48