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Merged
jfy133 merged 1 commit into from
Apr 2, 2025
Merged

Add threads parameter for all seqkit modules missing #8192

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21 changes: 11 additions & 10 deletions modules/nf-core/seqkit/concat/main.nf
View file
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Original file line number Diff line number Diff line change
@@ -1,30 +1,31 @@
process SEQKIT_CONCAT {
tag "$meta.id"
tag "${meta.id}"
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
: 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"

input:
tuple val(meta), path(input, stageAs: 'in/*')

output:
tuple val(meta), path("*.{fasta,fastq,fa,fq,fas,fna,faa}"), emit: fastx
path "versions.yml", emit: versions
path "versions.yml", emit: versions

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

script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def file_type = input instanceof List ? input[0].getExtension() : input.getExtension()
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def file_type = input instanceof List ? input[0].getExtension() : input.getExtension()
"""
seqkit \\
concat \\
$args \\
--threads ${task.cpus} \\
${args} \\
in/* > ${prefix}.${file_type}

cat <<-END_VERSIONS > versions.yml
Expand All @@ -34,7 +35,7 @@ process SEQKIT_CONCAT {
"""

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

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52 changes: 28 additions & 24 deletions modules/nf-core/seqkit/seq/main.nf
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Original file line number Diff line number Diff line change
@@ -1,41 +1,43 @@
process SEQKIT_SEQ {
tag "$meta.id"
tag "${meta.id}"
label 'process_low'
// File IO can be a bottleneck. See: https://bioinf.shenwei.me/seqkit/usage/#parallelization-of-cpu-intensive-jobs

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
: 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"

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

output:
tuple val(meta), path("${prefix}.*") , emit: fastx
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}.*"), emit: fastx
path "versions.yml", emit: versions

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

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
extension = "fasta"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
extension = "fasta"
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
def call_gzip = extension.endsWith('.gz') ? "| gzip -c ${args2}" : ''
if ("${prefix}.${extension}" == "${fastx}") {
error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
def call_gzip = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
seqkit \\
seq \\
--threads $task.cpus \\
$args \\
$fastx \\
$call_gzip \\
--threads ${task.cpus} \\
${args} \\
${fastx} \\
${call_gzip} \\
> ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
Expand All @@ -45,13 +47,15 @@ process SEQKIT_SEQ {
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
extension = "fasta"
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
extension = "fasta"
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${prefix}.${extension}" == "${fastx}") {
error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
}
"""
touch ${prefix}.${extension}

Expand Down
15 changes: 8 additions & 7 deletions modules/nf-core/seqkit/stats/main.nf
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Original file line number Diff line number Diff line change
@@ -1,18 +1,18 @@
process SEQKIT_STATS {
tag "$meta.id"
tag "${meta.id}"
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
: 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"

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

output:
tuple val(meta), path("*.tsv"), emit: stats
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -23,8 +23,9 @@ process SEQKIT_STATS {
"""
seqkit stats \\
--tabular \\
$args \\
$reads > '${prefix}.tsv'
--threads ${task.cpus} \\
${args} \\
${reads} > '${prefix}.tsv'

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
44 changes: 24 additions & 20 deletions modules/nf-core/seqkit/translate/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,33 +1,35 @@
process SEQKIT_TRANSLATE {
tag "$meta.id"
label 'process_single'
tag "${meta.id}"
label 'process_low'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
? 'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0'
: 'biocontainers/seqkit:2.9.0--h9ee0642_0'}"

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

output:
tuple val(meta), path("${prefix}.*"), emit: fastx
path "versions.yml" , emit: versions
path "versions.yml", emit: versions

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

script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
extension = "fasta"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
extension = "fasta"
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
def call_gzip = extension.endsWith('.gz') ? "| gzip -c ${args2}" : ''
if ("${prefix}.${extension}" == "${fastx}") {
error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
def call_gzip = extension.endsWith('.gz') ? "| gzip -c $args2" : ''
if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
"""
seqkit \\
translate \\
Expand All @@ -44,13 +46,15 @@ process SEQKIT_TRANSLATE {
"""

stub:
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) {
extension = "fasta"
prefix = task.ext.prefix ?: "${meta.id}"
def extension = "fastq"
if ("${fastx}" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/) {
extension = "fasta"
}
extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension
if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${prefix}.${extension}" == "${fastx}") {
error("Input and output names are the same, use \"task.ext.prefix\" to disambiguate!")
}
"""
touch ${prefix}.${extension}

Expand Down
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