From 226b6329b4ff21bf63afb1add84386d3a36883b3 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Thu, 16 May 2024 10:43:27 -0700 Subject: [PATCH] Remove --versioned_outdir param --- modules/bakta.nf | 2 +- modules/fastp.nf | 4 ++-- modules/long_read_qc.nf | 4 ++-- modules/prokka.nf | 2 +- modules/provenance.nf | 2 +- modules/quast.nf | 2 +- modules/unicycler.nf | 2 +- nextflow.config | 1 - 8 files changed, 9 insertions(+), 10 deletions(-) diff --git a/modules/bakta.nf b/modules/bakta.nf index 6956a3a..5dc44f9 100644 --- a/modules/bakta.nf +++ b/modules/bakta.nf @@ -4,7 +4,7 @@ process bakta { errorStrategy 'ignore' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}*.{gbk,gff,json,log}", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}*.{gbk,gff,json,log}", mode: 'copy' input: tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode) diff --git a/modules/fastp.nf b/modules/fastp.nf index df57f7a..5165f04 100644 --- a/modules/fastp.nf +++ b/modules/fastp.nf @@ -2,7 +2,7 @@ process fastp { tag { sample_id } - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.json", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.json", mode: 'copy' input: tuple val(sample_id), path(reads) @@ -40,7 +40,7 @@ process fastp_json_to_csv { executor 'local' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.csv", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_fastp.csv", mode: 'copy' input: tuple val(sample_id), path(fastp_json) diff --git a/modules/long_read_qc.nf b/modules/long_read_qc.nf index 4c3b745..b52c409 100644 --- a/modules/long_read_qc.nf +++ b/modules/long_read_qc.nf @@ -60,7 +60,7 @@ process merge_nanoq_reports { executor 'local' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_nanoq.csv", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_nanoq.csv", mode: 'copy' input: tuple val(sample_id), path(nanoq_pre_filter), path(nanoq_post_filter) @@ -82,7 +82,7 @@ process bandage { executor 'local' errorStrategy 'ignore' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_bandage.png", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_bandage.png", mode: 'copy' input: tuple val(sample_id), path(assembly_graph), val(assembler), val(assembly_mode) diff --git a/modules/prokka.nf b/modules/prokka.nf index 5d429a7..5c75277 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -4,7 +4,7 @@ process prokka { errorStrategy 'ignore' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_prokka.{gbk,gff}", mode: 'copy' input: tuple val(sample_id), path(assembly), val(assembler), val(assembly_mode) diff --git a/modules/provenance.nf b/modules/provenance.nf index e05c069..a7780f0 100644 --- a/modules/provenance.nf +++ b/modules/provenance.nf @@ -4,7 +4,7 @@ process collect_provenance { executor 'local' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy' input: tuple val(sample_id), path(provenance_files) diff --git a/modules/quast.nf b/modules/quast.nf index ca3b4d2..eedb37a 100644 --- a/modules/quast.nf +++ b/modules/quast.nf @@ -41,7 +41,7 @@ process parse_quast_report { executor 'local' - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_quast.csv", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_${assembler}_${assembly_mode}_quast.csv", mode: 'copy' input: tuple val(sample_id), path(quast_report), val(assembler), val(assembly_mode) diff --git a/modules/unicycler.nf b/modules/unicycler.nf index 182985e..598bf3f 100644 --- a/modules/unicycler.nf +++ b/modules/unicycler.nf @@ -2,7 +2,7 @@ process unicycler { tag { sample_id + ' / ' + assembly_mode } - publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_unicycler_${assembly_mode}.{fa,gfa,log}", mode: 'copy' + publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_unicycler_${assembly_mode}.{fa,gfa,log}", mode: 'copy' input: tuple val(sample_id), path(reads), val(assembly_mode) diff --git a/nextflow.config b/nextflow.config index 8dda4d1..22228f6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -23,7 +23,6 @@ params { filtlong_min_length = 1000 filtlong_keep_percent = 90 samplesheet_input = 'NO_FILE' - versioned_outdir = false pipeline_short_name = parsePipelineName(manifest.toMap().get('name')) pipeline_minor_version = parseMinorVersion(manifest.toMap().get('version')) }