From 3df3d671f26b8f309cb8d6bdc6c2bf838ff0597e Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Tue, 16 Mar 2021 17:16:47 +0000 Subject: [PATCH] Fix nf-core modules lint tests (#275) * Fix Conda definition bug * Add process label --- software/bismark/deduplicate/main.nf | 2 +- software/bismark/genome_preparation/main.nf | 2 +- software/cat/fastq/main.nf | 1 + software/gffread/main.nf | 1 + software/gunzip/main.nf | 1 + software/hisat2/build/main.nf | 1 + software/hisat2/extractsplicesites/main.nf | 1 + software/samtools/flagstat/main.nf | 1 + software/samtools/idxstats/main.nf | 1 + software/samtools/index/main.nf | 1 + software/samtools/stats/main.nf | 1 + software/samtools/view/main.nf | 1 + software/tabix/bgzip/main.nf | 1 + software/untar/main.nf | 1 + 14 files changed, 14 insertions(+), 2 deletions(-) diff --git a/software/bismark/deduplicate/main.nf b/software/bismark/deduplicate/main.nf index c75b868c..96f61c96 100644 --- a/software/bismark/deduplicate/main.nf +++ b/software/bismark/deduplicate/main.nf @@ -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 { diff --git a/software/bismark/genome_preparation/main.nf b/software/bismark/genome_preparation/main.nf index 8c98de15..17f517af 100644 --- a/software/bismark/genome_preparation/main.nf +++ b/software/bismark/genome_preparation/main.nf @@ -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 { diff --git a/software/cat/fastq/main.nf b/software/cat/fastq/main.nf index b3f01af9..ed62e432 100644 --- a/software/cat/fastq/main.nf +++ b/software/cat/fastq/main.nf @@ -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) } diff --git a/software/gffread/main.nf b/software/gffread/main.nf index d0a4e02f..e9290888 100644 --- a/software/gffread/main.nf +++ b/software/gffread/main.nf @@ -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:'') } diff --git a/software/gunzip/main.nf b/software/gunzip/main.nf index d3159aa2..d6bbe045 100644 --- a/software/gunzip/main.nf +++ b/software/gunzip/main.nf @@ -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:'') } diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf index f1c83f99..b8642ef3 100644 --- a/software/hisat2/build/main.nf +++ b/software/hisat2/build/main.nf @@ -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:'') } diff --git a/software/hisat2/extractsplicesites/main.nf b/software/hisat2/extractsplicesites/main.nf index a88c2e50..b40a97da 100644 --- a/software/hisat2/extractsplicesites/main.nf +++ b/software/hisat2/extractsplicesites/main.nf @@ -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:'') } diff --git a/software/samtools/flagstat/main.nf b/software/samtools/flagstat/main.nf index 863be3d8..bb3663f6 100644 --- a/software/samtools/flagstat/main.nf +++ b/software/samtools/flagstat/main.nf @@ -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) } diff --git a/software/samtools/idxstats/main.nf b/software/samtools/idxstats/main.nf index 99fa9853..80f97630 100644 --- a/software/samtools/idxstats/main.nf +++ b/software/samtools/idxstats/main.nf @@ -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) } diff --git a/software/samtools/index/main.nf b/software/samtools/index/main.nf index b4fd1347..86114fc7 100644 --- a/software/samtools/index/main.nf +++ b/software/samtools/index/main.nf @@ -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) } diff --git a/software/samtools/stats/main.nf b/software/samtools/stats/main.nf index c16fbe88..f5302d08 100644 --- a/software/samtools/stats/main.nf +++ b/software/samtools/stats/main.nf @@ -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) } diff --git a/software/samtools/view/main.nf b/software/samtools/view/main.nf index befaf5a6..2ec29a42 100644 --- a/software/samtools/view/main.nf +++ b/software/samtools/view/main.nf @@ -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) } diff --git a/software/tabix/bgzip/main.nf b/software/tabix/bgzip/main.nf index 5aefbc75..6960812f 100644 --- a/software/tabix/bgzip/main.nf +++ b/software/tabix/bgzip/main.nf @@ -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) } diff --git a/software/untar/main.nf b/software/untar/main.nf index e1594263..b0fc0cd9 100644 --- a/software/untar/main.nf +++ b/software/untar/main.nf @@ -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:'') }