From 65a34226864d58c9eda4fda3ce3b0f3528c53f94 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Sat, 10 Apr 2021 20:49:09 +0100 Subject: [PATCH] Add default publish_dir for index processes (#428) --- software/bowtie/build/main.nf | 2 +- software/bowtie2/build/main.nf | 2 +- software/bwa/index/main.nf | 2 +- software/bwamem2/index/main.nf | 2 +- software/bwameth/index/main.nf | 2 +- software/cat/fastq/main.nf | 2 +- software/hisat2/build/main.nf | 2 +- software/rsem/preparereference/main.nf | 2 +- software/salmon/index/main.nf | 2 +- software/star/genomegenerate/main.nf | 2 +- software/yara/index/main.nf | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) diff --git a/software/bowtie/build/main.nf b/software/bowtie/build/main.nf index b248b18a..3a6071a9 100644 --- a/software/bowtie/build/main.nf +++ b/software/bowtie/build/main.nf @@ -9,7 +9,7 @@ process BOWTIE_BUILD { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/bowtie2/build/main.nf b/software/bowtie2/build/main.nf index 922ca35a..42ff1d20 100644 --- a/software/bowtie2/build/main.nf +++ b/software/bowtie2/build/main.nf @@ -9,7 +9,7 @@ process BOWTIE2_BUILD { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf index d103ca1f..aabd187c 100644 --- a/software/bwa/index/main.nf +++ b/software/bwa/index/main.nf @@ -9,7 +9,7 @@ process BWA_INDEX { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/bwamem2/index/main.nf b/software/bwamem2/index/main.nf index 6b7ab02d..b667f266 100644 --- a/software/bwamem2/index/main.nf +++ b/software/bwamem2/index/main.nf @@ -9,7 +9,7 @@ process BWAMEM2_INDEX { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/bwameth/index/main.nf b/software/bwameth/index/main.nf index f7a26e4b..dbea0ae4 100644 --- a/software/bwameth/index/main.nf +++ b/software/bwameth/index/main.nf @@ -9,7 +9,7 @@ process BWAMETH_INDEX { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::bwameth=0.2.2" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/cat/fastq/main.nf b/software/cat/fastq/main.nf index 99a2a846..55ccca90 100644 --- a/software/cat/fastq/main.nf +++ b/software/cat/fastq/main.nf @@ -9,7 +9,7 @@ process CAT_FASTQ { label 'process_low' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', meta:meta, publish_by_meta:['id']) } conda (params.enable_conda ? "conda-forge::sed=4.7" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/hisat2/build/main.nf b/software/hisat2/build/main.nf index bb595dcd..e74c8cae 100644 --- a/software/hisat2/build/main.nf +++ b/software/hisat2/build/main.nf @@ -11,7 +11,7 @@ process HISAT2_BUILD { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::hisat2=2.2.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/rsem/preparereference/main.nf b/software/rsem/preparereference/main.nf index 3625050a..a378eb6b 100644 --- a/software/rsem/preparereference/main.nf +++ b/software/rsem/preparereference/main.nf @@ -9,7 +9,7 @@ process RSEM_PREPAREREFERENCE { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/salmon/index/main.nf b/software/salmon/index/main.nf index c9d6df5f..17d5bc06 100644 --- a/software/salmon/index/main.nf +++ b/software/salmon/index/main.nf @@ -9,7 +9,7 @@ process SALMON_INDEX { label "process_medium" publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { diff --git a/software/star/genomegenerate/main.nf b/software/star/genomegenerate/main.nf index 4abae682..fb1feea8 100644 --- a/software/star/genomegenerate/main.nf +++ b/software/star/genomegenerate/main.nf @@ -9,7 +9,7 @@ process STAR_GENOMEGENERATE { label 'process_high' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } // Note: 2.7X indices incompatible with AWS iGenomes. conda (params.enable_conda ? "bioconda::star=2.6.1d" : null) diff --git a/software/yara/index/main.nf b/software/yara/index/main.nf index e03552d8..f1fe13a5 100644 --- a/software/yara/index/main.nf +++ b/software/yara/index/main.nf @@ -9,7 +9,7 @@ process YARA_INDEX { label 'process_medium' publishDir "${params.outdir}", mode: params.publish_dir_mode, - saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) } + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) } conda (params.enable_conda ? "bioconda::yara=1.0.2" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {