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Add --paired flag to umitools dedup and bump to 1.1.2 (#583)

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* Add --paired flag to umitools dedup and bump to 1.1.2

* paired not paired_end

* Fix ECLint
This commit is contained in:
Harshil Patel 2021-07-16 14:21:08 +01:00 committed by GitHub
parent adfb8a3d65
commit 2ade120249
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 12 additions and 12 deletions
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14
modules/umitools/dedup/main.nf
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@ -11,11 +11,11 @@ process UMITOOLS_DEDUP {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null) conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1" container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
} else { } else {
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1" container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
} }
input: input:
@ -23,19 +23,19 @@ process UMITOOLS_DEDUP {
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam
tuple val(meta), path("*.tsv"), emit: tsv
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def paired = meta.single_end ? "" : "--paired"
""" """
umi_tools dedup \\ umi_tools dedup \\
-I $bam \\ -I $bam \\
-S ${prefix}.bam \\ -S ${prefix}.bam \\
--output-stats=$prefix \\ $paired \\
$options.args \\ $options.args
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
""" """
} }

10
modules/umitools/extract/main.nf
View file

@ -11,11 +11,11 @@ process UMITOOLS_EXTRACT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::umi_tools=1.1.1" : null) conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.1--py38h0213d0e_1" container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
} else { } else {
container "quay.io/biocontainers/umi_tools:1.1.1--py38h0213d0e_1" container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
} }
input: input:
@ -38,7 +38,7 @@ process UMITOOLS_EXTRACT {
$options.args \\ $options.args \\
> ${prefix}.umi_extract.log > ${prefix}.umi_extract.log
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
""" """
} else { } else {
""" """
@ -51,7 +51,7 @@ process UMITOOLS_EXTRACT {
$options.args \\ $options.args \\
> ${prefix}.umi_extract.log > ${prefix}.umi_extract.log
umi_tools --version | sed -e "s/UMI-tools version: //g" > ${software}.version.txt echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
""" """
} }
} }