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Fgbio tmpdir modification (#1890)

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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

* Changed tmp-dir to .

* Update modules/fgbio/groupreadsbyumi/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Update modules/fgbio/fastqtobam/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* Added callmol and sortbam

* fixed typo in callmol container

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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WackerO 2022-07-15 11:20:58 +02:00 committed by GitHub
parent 1368164eb5
commit 6720d88f4e
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4 changed files with 7 additions and 7 deletions
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1
modules/fgbio/callmolecularconsensusreads/main.nf
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@ -22,6 +22,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
fgbio \\ fgbio \\
--tmp-dir=. \\
CallMolecularConsensusReads \\ CallMolecularConsensusReads \\
-i $bam \\ -i $bam \\
$args \\ $args \\

3
modules/fgbio/fastqtobam/main.nf
View file

@ -22,10 +22,9 @@ process FGBIO_FASTQTOBAM {
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
mkdir tmp
fgbio \\ fgbio \\
--tmp-dir=${PWD}/tmp \\ --tmp-dir=. \\
FastqToBam \\ FastqToBam \\
-i $reads \\ -i $reads \\
-o "${prefix}_umi_converted.bam" \\ -o "${prefix}_umi_converted.bam" \\

3
modules/fgbio/groupreadsbyumi/main.nf
View file

@ -24,10 +24,9 @@ process FGBIO_GROUPREADSBYUMI {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
mkdir tmp
fgbio \\ fgbio \\
--tmp-dir=${PWD}/tmp \\ --tmp-dir=. \\
GroupReadsByUmi \\ GroupReadsByUmi \\
-s $strategy \\ -s $strategy \\
$args \\ $args \\

7
modules/fgbio/sortbam/main.nf
View file

@ -2,10 +2,10 @@ process FGBIO_SORTBAM {
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)
@ -22,6 +22,7 @@ process FGBIO_SORTBAM {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
""" """
fgbio \\ fgbio \\
--tmp-dir=. \\
SortBam \\ SortBam \\
-i $bam \\ -i $bam \\
$args \\ $args \\