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Update PyDamage module (#1467)

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* add pydamage module

* remove TODOs

* split module by subcommands

* update version parsing

* remove forgotten TODOs

* update module names

* remove old holistic module

* Update modules/pydamage/analyze/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add keywords

* update resource requirement

* Update modules/pydamage/filter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/pydamage/filter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* merge from upstream

* update pydamage from upstream

* add freebayes

* update pydamage test from upstream

* fix meta.yml

* update functions.nf

* update test.yml

* update version parsing

* update version parsing

* fix indentation

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs

* Update modules/freebayes/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add bed test

* add metabat2 module

* only freebayes

* remove metabat2

* update md5sum because of vcf including date of the day

* add keyword

* rescue conflicted files

* attempt to fix ECLint

* add pytest workflow for metabat

* remove -

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* add optional inputs/outpus

* remove trailing whitespace

* compressing and removing not reproducible md5sums

* follow symlinks while decompressing

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* split tests

* export env variable

* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/metabat2/metabat2/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* answer PR comments and switch to bgzip

* add bacillus fragilis alignments

* add meta to samtools/faidx

* move to bgzip

* update freebayes test results

* bump pydamage version to 0.70

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
This commit is contained in:
Maxime Borry 2022-03-31 15:18:18 +02:00 committed by GitHub
parent 794f84534b
commit 64b06baa06
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2 changed files with 6 additions and 6 deletions
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6
modules/pydamage/analyze/main.nf
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@ -2,10 +2,10 @@ process PYDAMAGE_ANALYZE {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null) conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' : 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }" 'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(bam), path(bai) tuple val(meta), path(bam), path(bai)

6
modules/pydamage/filter/main.nf
View file

@ -2,10 +2,10 @@ process PYDAMAGE_FILTER {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null) conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' : 'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }" 'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(csv) tuple val(meta), path(csv)