mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-11 00:03:09 +00:00
chore: force update all modules
This commit is contained in:
parent
fdb8a7f740
commit
b407fbcdce
19 changed files with 80 additions and 39 deletions
10
modules/nf-core/cat/fastq/main.nf
generated
10
modules/nf-core/cat/fastq/main.nf
generated
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@ -1,6 +1,6 @@
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process CAT_FASTQ {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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@ -20,9 +20,9 @@ process CAT_FASTQ {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def readList = reads.collect{ it.toString() }
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def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
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if (meta.single_end) {
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if (readList.size > 1) {
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if (readList.size >= 1) {
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"""
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cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
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@ -33,7 +33,7 @@ process CAT_FASTQ {
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"""
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}
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} else {
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if (readList.size > 2) {
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if (readList.size >= 2) {
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def read1 = []
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def read2 = []
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readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
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@ -51,7 +51,7 @@ process CAT_FASTQ {
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def readList = reads.collect{ it.toString() }
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def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
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if (meta.single_end) {
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if (readList.size > 1) {
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"""
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2
modules/nf-core/centrifuge/kreport/main.nf
generated
2
modules/nf-core/centrifuge/kreport/main.nf
generated
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@ -1,6 +1,6 @@
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process CENTRIFUGE_KREPORT {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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@ -58,11 +58,12 @@ versions_by_module = {}
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for process, process_versions in versions_by_process.items():
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module = process.split(":")[-1]
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try:
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assert versions_by_module[module] == process_versions, (
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"We assume that software versions are the same between all modules. "
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"If you see this error-message it means you discovered an edge-case "
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"and should open an issue in nf-core/tools. "
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)
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if versions_by_module[module] != process_versions:
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raise AssertionError(
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"We assume that software versions are the same between all modules. "
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"If you see this error-message it means you discovered an edge-case "
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"and should open an issue in nf-core/tools. "
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)
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except KeyError:
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versions_by_module[module] = process_versions
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2
modules/nf-core/eido/convert/main.nf
generated
2
modules/nf-core/eido/convert/main.nf
generated
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@ -1,5 +1,5 @@
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process EIDO_CONVERT {
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tag '$samplesheet'
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tag "$samplesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
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2
modules/nf-core/eido/validate/main.nf
generated
2
modules/nf-core/eido/validate/main.nf
generated
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@ -1,5 +1,5 @@
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process EIDO_VALIDATE {
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tag '$samplesheet'
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tag "$samplesheet"
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::eido=0.1.9" : null)
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2
modules/nf-core/gunzip/main.nf
generated
2
modules/nf-core/gunzip/main.nf
generated
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@ -1,6 +1,6 @@
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process GUNZIP {
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tag "$archive"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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2
modules/nf-core/kaiju/kaiju2krona/main.nf
generated
2
modules/nf-core/kaiju/kaiju2krona/main.nf
generated
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@ -1,6 +1,6 @@
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process KAIJU_KAIJU2KRONA {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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2
modules/nf-core/kaiju/kaiju2table/main.nf
generated
2
modules/nf-core/kaiju/kaiju2table/main.nf
generated
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@ -1,6 +1,6 @@
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process KAIJU_KAIJU2TABLE {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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@ -1,5 +1,5 @@
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process KRAKENTOOLS_COMBINEKREPORTS {
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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@ -1,6 +1,6 @@
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process KRAKENTOOLS_KREPORT2KRONA {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
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2
modules/nf-core/krona/ktimporttaxonomy/main.nf
generated
2
modules/nf-core/krona/ktimporttaxonomy/main.nf
generated
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@ -1,6 +1,6 @@
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process KRONA_KTIMPORTTAXONOMY {
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tag "${meta.id}"
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label 'process_high'
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label 'process_single'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::krona=2.8" : null)
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2
modules/nf-core/krona/ktimporttext/main.nf
generated
2
modules/nf-core/krona/ktimporttext/main.nf
generated
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@ -1,6 +1,6 @@
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process KRONA_KTIMPORTTEXT {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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2
modules/nf-core/megan/rma2info/main.nf
generated
2
modules/nf-core/megan/rma2info/main.nf
generated
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@ -1,6 +1,6 @@
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process MEGAN_RMA2INFO {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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6
modules/nf-core/minimap2/index/main.nf
generated
6
modules/nf-core/minimap2/index/main.nf
generated
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@ -7,11 +7,11 @@ process MINIMAP2_INDEX {
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'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
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input:
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path fasta
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tuple val(meta), path(fasta)
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output:
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path "*.mmi" , emit: index
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.mmi"), emit: index
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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10
modules/nf-core/minimap2/index/meta.yml
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10
modules/nf-core/minimap2/index/meta.yml
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@ -12,11 +12,21 @@ tools:
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documentation: https://github.com/lh3/minimap2#uguide
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: |
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Reference database in FASTA format.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- mmi:
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type: file
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description: Minimap2 fasta index.
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2
modules/nf-core/motus/merge/main.nf
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2
modules/nf-core/motus/merge/main.nf
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@ -2,7 +2,7 @@ VERSION = '3.0.1'
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process MOTUS_MERGE {
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tag "$meta.id"
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label 'process_low'
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label 'process_single'
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conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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26
modules/nf-core/samtools/view/main.nf
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26
modules/nf-core/samtools/view/main.nf
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@ -10,31 +10,39 @@ process SAMTOOLS_VIEW {
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input:
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tuple val(meta), path(input), path(index)
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path fasta
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path qname
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output:
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tuple val(meta), path("*.bam") , emit: bam , optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.bam"), emit: bam, optional: true
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tuple val(meta), path("*.cram"), emit: cram, optional: true
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tuple val(meta), path("*.sam"), emit: sam, optional: true
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tuple val(meta), path("*.bai"), emit: bai, optional: true
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tuple val(meta), path("*.csi"), emit: csi, optional: true
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tuple val(meta), path("*.crai"), emit: crai, optional: true
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "--reference ${fasta} -C" : ""
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def file_type = input.getExtension()
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def reference = fasta ? "--reference ${fasta}" : ""
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def readnames = qname ? "--qname-file ${qname}": ""
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def file_type = args.contains("--output-fmt sam") ? "sam" :
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args.contains("--output-fmt bam") ? "bam" :
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args.contains("--output-fmt cram") ? "cram" :
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input.getExtension()
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if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
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"""
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samtools \\
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view \\
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--threads ${task.cpus-1} \\
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${reference} \\
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${readnames} \\
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$args \\
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$input \\
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$args2 \\
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> ${prefix}.${file_type}
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-o ${prefix}.${file_type} \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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30
modules/nf-core/samtools/view/meta.yml
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30
modules/nf-core/samtools/view/meta.yml
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@ -33,6 +33,10 @@ input:
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type: optional file
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description: Reference file the CRAM was created with
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pattern: "*.{fasta,fa}"
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- qname:
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type: file
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description: Optional file with read names to output only select alignments
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pattern: "*.{txt,list}"
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output:
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- meta:
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type: map
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: filtered/converted BAM/SAM file
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pattern: "*.{bam,sam}"
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description: optional filtered/converted BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: filtered/converted CRAM file
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pattern: "*.cram"
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description: optional filtered/converted CRAM file
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pattern: "*.{cram}"
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- sam:
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type: file
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description: optional filtered/converted SAM file
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pattern: "*.{sam}"
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# bai, csi, and crai are created with `--write-index`
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- bai:
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type: file
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description: optional BAM file index
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pattern: "*.{bai}"
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- csi:
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type: file
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description: optional tabix BAM file index
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pattern: "*.{csi}"
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- crai:
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type: file
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description: optional CRAM file index
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pattern: "*.{crai}"
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- versions:
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type: file
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description: File containing software versions
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@ -55,3 +76,4 @@ authors:
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- "@drpatelh"
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- "@joseespinosa"
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- "@FriederikeHanssen"
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- "@priyanka-surana"
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2
modules/nf-core/untar/main.nf
generated
2
modules/nf-core/untar/main.nf
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@ -27,7 +27,7 @@ process UNTAR {
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## Ensures --strip-components only applied when top level of tar contents is a directory
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## If just files or multiple directories, place all in output
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if [[ \$(tar -tzf ${archive} | grep "/\$" | wc -l) -eq 1 ]]; then
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if [[ \$(tar -tzf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
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tar \\
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-C output --strip-components 1 \\
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-xzvf \\
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