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Merged
jonasscheid merged 2 commits into from
Apr 28, 2025
Merged

Harmonize indents #366

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7e95685
Harmonize indents
jonasscheid Apr 27, 2025
9917c20
pin nf-schema to 2.2.0
jonasscheid Apr 28, 2025
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2 changes: 1 addition & 1 deletion modules/local/datamash_histogram.nf
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Expand Up @@ -39,8 +39,8 @@ process DATAMASH_HISTOGRAM {
"""

stub:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}_binned.tsv

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1 change: 0 additions & 1 deletion modules/local/easypqp/library.nf
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Expand Up @@ -38,7 +38,6 @@ process EASYPQP_LIBRARY {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
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1 change: 0 additions & 1 deletion modules/local/ms2rescore.nf
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Expand Up @@ -41,7 +41,6 @@ process MS2RESCORE {
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_ms2rescore"

"""
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41 changes: 20 additions & 21 deletions modules/local/openms_featurefinderidentification.nf
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Expand Up @@ -12,33 +12,32 @@ process OPENMS_FEATUREFINDERIDENTIFICATION {
tuple val(meta), path(mzml), path(id_int), path(id_ext)

output:
tuple val(meta), path("*.featureXML"), emit: featurexml
path "versions.yml" , emit: versions
tuple val(meta), path("*.featureXML"), emit: featurexml
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
task.ext.when == null || task.ext.when

script:
def prefix = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}"
def args = task.ext.args ?: ''
def quant_fdr = params.quantification_fdr ? "-id $id_int -id_ext $id_ext -svm:min_prob ${params.quantification_min_prob}" : "-id $id_ext"
args = args + " $quant_fdr"

"""
FeatureFinderIdentification -in $mzml \\
-out ${prefix}.featureXML \\
-threads $task.cpus \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
def prefix = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}"
def args = task.ext.args ?: ''
def quant_fdr = params.quantification_fdr ? "-id $id_int -id_ext $id_ext -svm:min_prob ${params.quantification_min_prob}" : "-id $id_ext"
args = args + " $quant_fdr"

"""
FeatureFinderIdentification -in $mzml \\
-out ${prefix}.featureXML \\
-threads $task.cpus \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}"

"""
touch ${prefix}.featureXML
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44 changes: 22 additions & 22 deletions modules/local/openms_featurelinkerunlabeledkd.nf
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Expand Up @@ -8,38 +8,38 @@ process OPENMS_FEATURELINKERUNLABELEDKD {
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(features)
tuple val(meta), path(features)

output:
tuple val(meta), path("*.consensusXML"), emit: consensusxml
path "versions.yml" , emit: versions
tuple val(meta), path("*.consensusXML"), emit: consensusxml
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
task.ext.when == null || task.ext.when

script:
def prefix = task.ext.prefix ?: "${meta.id}_all_features_merged"
def prefix = task.ext.prefix ?: "${meta.id}_all_features_merged"

"""
FeatureLinkerUnlabeledKD -in $features \\
-out ${prefix}.consensusXML \\
-threads $task.cpus
"""
FeatureLinkerUnlabeledKD -in $features \\
-out ${prefix}.consensusXML \\
-threads $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}_all_features_merged"
def prefix = task.ext.prefix ?: "${meta.id}_all_features_merged"

"""
touch ${prefix}.consensusXML
"""
touch ${prefix}.consensusXML

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
}
45 changes: 23 additions & 22 deletions modules/local/openms_idconflictresolver.nf
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Expand Up @@ -8,38 +8,39 @@ process OPENMS_IDCONFLICTRESOLVER {
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(consensus)
tuple val(meta), path(consensus)

output:
tuple val(meta), path("*.consensusXML"), emit: consensusxml
path "versions.yml" , emit: versions
tuple val(meta), path("*.consensusXML"), emit: consensusxml
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
task.ext.when == null || task.ext.when

script:
def prefix = task.ext.prefix ?: "${meta.id}_resolved"
def prefix = task.ext.prefix ?: "${meta.id}_resolved"

"""
IDConflictResolver -in $consensus \\
-out ${prefix}.consensusXML \\
-threads $task.cpus
"""
IDConflictResolver \\
-in $consensus \\
-out ${prefix}.consensusXML \\
-threads $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}_resolved"
def prefix = task.ext.prefix ?: "${meta.id}_resolved"

"""
touch ${prefix}.consensusXML
"""
touch ${prefix}.consensusXML

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
}
53 changes: 26 additions & 27 deletions modules/local/openms_mapaligneridentification.nf
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Expand Up @@ -8,41 +8,40 @@ process OPENMS_MAPALIGNERIDENTIFICATION {
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(idxmls)
tuple val(meta), path(idxmls)

output:
tuple val(meta), path("*.trafoXML"), emit: trafoxml
path "versions.yml" , emit: versions
tuple val(meta), path("*.trafoXML"), emit: trafoxml
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
task.ext.when == null || task.ext.when

script:
def out_names = idxmls.collect { it.baseName.replace('_fdr_filtered','')+'.trafoXML' }.join(' ')
def args = task.ext.args ?: ''
def args = task.ext.args ?: ''
def out_names = idxmls.collect { it.baseName.replace('_fdr_filtered','')+'.trafoXML' }.join(' ')

"""
MapAlignerIdentification -in $idxmls \\
-trafo_out ${out_names} \\
$args
"""
MapAlignerIdentification \\
-in $idxmls \\
-trafo_out ${out_names} \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

stub:
def out_names = idxmls.collect { it.baseName.replace('_fdr_filtered','')+'.trafoXML' }.join(' ')
def args = task.ext.args ?: ''

"""
touch test1.consensusXML
touch test2.consensusXML

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

"""
touch test1.consensusXML
touch test2.consensusXML

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
}
57 changes: 30 additions & 27 deletions modules/local/openms_maprttransformer.nf
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Expand Up @@ -8,41 +8,44 @@ process OPENMS_MAPRTTRANSFORMER {
'biocontainers/openms:3.3.0--h0656172_8' }"

input:
tuple val(meta), path(alignment_file), path(trafoxml)
tuple val(meta), path(alignment_file), path(trafoxml)

output:
tuple val(meta), path("*_aligned.*"), emit: aligned
path "versions.yml" , emit: versions
tuple val(meta), path("*_aligned.*"), emit: aligned
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
task.ext.when == null || task.ext.when

script:
def prefix = task.ext.prefix ?: "${meta.id}"
def fileExt = alignment_file.collect { it.name.tokenize("\\.")[1] }.join(' ')

"""
MapRTTransformer -in $alignment_file \\
-trafo_in $trafoxml \\
-out ${prefix}.${fileExt} \\
-threads $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def fileExt = alignment_file.collect { it.name.tokenize("\\.")[1] }.join(' ')

"""
MapRTTransformer \\
-in $alignment_file \\
-trafo_in $trafoxml \\
-out ${prefix}.${fileExt} \\
-threads $task.cpus \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
def fileExt = alignment_file.collect { it.name.tokenize("\\.")[1] }.join(' ')
def prefix = task.ext.prefix ?: "${meta.id}"
def fileExt = alignment_file.collect { it.name.tokenize("\\.")[1] }.join(' ')

"""
touch ${prefix}.${fileExt}
"""
touch ${prefix}.${fileExt}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
END_VERSIONS
"""
}
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