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Fix nf-core modules lint tests (#275)

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* Fix Conda definition bug

* Add process label
This commit is contained in:
Harshil Patel 2021-03-16 17:16:47 +00:00 committed by GitHub
parent 74ff11b07b
commit 3df3d671f2
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GPG key ID: 4AEE18F83AFDEB23
14 changed files with 14 additions and 2 deletions
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2
software/bismark/deduplicate/main.nf
View file

@ -11,7 +11,7 @@ process BISMARK_DEDUPLICATE {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bismark==0.23.0" : null)
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
} else {

2
software/bismark/genome_preparation/main.nf
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@ -11,7 +11,7 @@ process BISMARK_GENOME_PREPARATION {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bismark==0.23.0" : null)
conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
} else {

1
software/cat/fastq/main.nf
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@ -6,6 +6,7 @@ options = initOptions(params.options)
process CAT_FASTQ {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', publish_id:meta.id) }

1
software/gffread/main.nf
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@ -6,6 +6,7 @@ options = initOptions(params.options)
process GFFREAD {
tag "$gff"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

1
software/gunzip/main.nf
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@ -6,6 +6,7 @@ options = initOptions(params.options)
process GUNZIP {
tag "$archive"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

1
software/hisat2/build/main.nf
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@ -8,6 +8,7 @@ def VERSION = '2.2.0'
process HISAT2_BUILD {
tag "$fasta"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

1
software/hisat2/extractsplicesites/main.nf
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@ -8,6 +8,7 @@ def VERSION = '2.2.0'
process HISAT2_EXTRACTSPLICESITES {
tag "$gtf"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }

1
software/samtools/flagstat/main.nf
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@ -6,6 +6,7 @@ options = initOptions(params.options)
process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/samtools/idxstats/main.nf
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@ -6,6 +6,7 @@ options = initOptions(params.options)
process SAMTOOLS_IDXSTATS {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/samtools/index/main.nf
View file

@ -6,6 +6,7 @@ options = initOptions(params.options)
process SAMTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/samtools/stats/main.nf
View file

@ -6,6 +6,7 @@ options = initOptions(params.options)
process SAMTOOLS_STATS {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/samtools/view/main.nf
View file

@ -6,6 +6,7 @@ options = initOptions(params.options)
process SAMTOOLS_VIEW {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/tabix/bgzip/main.nf
View file

@ -6,6 +6,7 @@ options = initOptions(params.options)
process TABIX_BGZIP {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }

1
software/untar/main.nf
View file

@ -6,6 +6,7 @@ options = initOptions(params.options)
process UNTAR {
tag "$archive"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }