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Code Issues Releases Packages Activity

Add default publish_dir for index processes (#428)

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Harshil Patel 2021-04-10 20:49:09 +01:00 committed by GitHub
parent 212177d479
commit 65a3422686
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11 changed files with 11 additions and 11 deletions
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2
software/bowtie/build/main.nf
View file

@ -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) {

2
software/bowtie2/build/main.nf
View file

@ -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) {

2
software/bwa/index/main.nf
View file

@ -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) {

2
software/bwamem2/index/main.nf
View file

@ -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) {

2
software/bwameth/index/main.nf
View file

@ -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) {

2
software/cat/fastq/main.nf
View file

@ -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) {

2
software/hisat2/build/main.nf
View file

@ -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) {

2
software/rsem/preparereference/main.nf
View file

@ -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) {

2
software/salmon/index/main.nf
View file

@ -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) {

2
software/star/genomegenerate/main.nf
View file

@ -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)

2
software/yara/index/main.nf
View file

@ -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) {