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Updated container versions for fgbio (#1878)

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* Updated container versions for fgbio groupreadsbyumi and callmolecularconsensusreads

* Corrected fgbio call container, trying to fix fgbio group tests

* Removed incorrect line
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WackerO 2022-07-14 13:51:34 +02:00 committed by GitHub
parent 9294259eea
commit c29b3fe11a
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4 changed files with 9 additions and 9 deletions
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6
modules/fgbio/callmolecularconsensusreads/main.nf
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@ -2,10 +2,10 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::fgbio=1.3.0" : null) conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : 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/fgbio:1.3.0--0' : 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
'quay.io/biocontainers/fgbio:1.3.0--0' }" 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)

6
modules/fgbio/groupreadsbyumi/main.nf
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@ -2,10 +2,10 @@ process FGBIO_GROUPREADSBYUMI {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_low'
conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null) conda (params.enable_conda ? "bioconda::fgbio=2.0.2" : 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/fgbio:1.4.0--hdfd78af_0' : 'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }" 'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"
input: input:
tuple val(meta), path(taggedbam) tuple val(meta), path(taggedbam)

2
tests/modules/fgbio/callmolecularconsensusreads/test.yml
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@ -5,6 +5,6 @@
- fgbio/callmolecularconsensusreads - fgbio/callmolecularconsensusreads
files: files:
- path: output/fgbio/test_molreads.bam - path: output/fgbio/test_molreads.bam
md5sum: 7010bcdc037c36af13dbc370c06c76d3 md5sum: 6ae57429e3218f5eba9555d597b7c60f
- path: output/fgbio/test_out.bam - path: output/fgbio/test_out.bam
md5sum: d84e28fecc90c0752c543e934f10aa31 md5sum: d84e28fecc90c0752c543e934f10aa31

4
tests/modules/fgbio/groupreadsbyumi/test.yml
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@ -5,6 +5,6 @@
- fgbio/groupreadsbyumi - fgbio/groupreadsbyumi
files: files:
- path: output/fgbio/test_umi-grouped.bam - path: output/fgbio/test_umi-grouped.bam
md5sum: f1e53fc845fd99a3da172eb8063dff0b md5sum: c7a9aee0b9b277c85d6a112d3021082d
- path: output/fgbio/test_umi_histogram.txt - path: output/fgbio/test_umi_histogram.txt
md5sum: d17fd167b2a765d46e4b01bf08ece01b md5sum: f2f29523bb7016e1a78fe634466cbfba