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Fgbio tmpdir modification #1890

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merged 14 commits into from
Jul 15, 2022
Merged

Fgbio tmpdir modification #1890

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9cae51e
Updated container versions for fgbio groupreadsbyumi and callmolecula…
WackerO Jul 13, 2022
900218c
Merge branch 'nf-core:master' into master
WackerO Jul 14, 2022
298c9b6
Corrected fgbio call container, trying to fix fgbio group tests
WackerO Jul 14, 2022
b02075c
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 14, 2022
6a653f7
Removed incorrect line
WackerO Jul 14, 2022
7de8719
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 14, 2022
caa369b
Merge branch 'master' of https://github.com/nf-core/modules
WackerO Jul 15, 2022
da4782f
Changed tmp-dir to .
WackerO Jul 15, 2022
458e206
Update modules/fgbio/groupreadsbyumi/main.nf
WackerO Jul 15, 2022
9b1f47b
Update modules/fgbio/fastqtobam/main.nf
WackerO Jul 15, 2022
fff912b
Added callmol and sortbam
WackerO Jul 15, 2022
f47ccf2
Merge branch 'fgbio_error' of https://github.com/WackerO/modules into…
WackerO Jul 15, 2022
de08233
fixed typo in callmol container
WackerO Jul 15, 2022
e98c9cb
Merge branch 'master' of https://github.com/nf-core/modules into fgbi…
WackerO Jul 15, 2022
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1 change: 1 addition & 0 deletions modules/fgbio/callmolecularconsensusreads/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
fgbio \\
--tmp-dir=. \\
CallMolecularConsensusReads \\
-i $bam \\
$args \\
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3 changes: 1 addition & 2 deletions modules/fgbio/fastqtobam/main.nf
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Expand Up @@ -22,10 +22,9 @@ process FGBIO_FASTQTOBAM {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir tmp

fgbio \\
--tmp-dir=${PWD}/tmp \\
--tmp-dir=. \\
FastqToBam \\
-i $reads \\
-o "${prefix}_umi_converted.bam" \\
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3 changes: 1 addition & 2 deletions modules/fgbio/groupreadsbyumi/main.nf
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Expand Up @@ -24,10 +24,9 @@ process FGBIO_GROUPREADSBYUMI {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
mkdir tmp

fgbio \\
--tmp-dir=${PWD}/tmp \\
--tmp-dir=. \\
GroupReadsByUmi \\
-s $strategy \\
$args \\
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7 changes: 4 additions & 3 deletions modules/fgbio/sortbam/main.nf
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Expand Up @@ -2,10 +2,10 @@ process FGBIO_SORTBAM {
tag "$meta.id"
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 ?
'https://depot.galaxyproject.org/singularity/fgbio:1.3.0--0' :
'quay.io/biocontainers/fgbio:1.3.0--0' }"
'https://depot.galaxyproject.org/singularity/fgbio:2.0.2--hdfd78af_0' :
'quay.io/biocontainers/fgbio:2.0.2--hdfd78af_0' }"

input:
tuple val(meta), path(bam)
Expand All @@ -22,6 +22,7 @@ process FGBIO_SORTBAM {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
fgbio \\
--tmp-dir=. \\
SortBam \\
-i $bam \\
$args \\
Expand Down