From d94534e8acee01575b589e88549ed64ab4fc4411 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Thu, 5 May 2022 09:07:33 +0200 Subject: [PATCH] Simplify params which control host removal publish --- conf/modules.config | 8 ++++---- nextflow.config | 6 +----- nextflow_schema.json | 16 ---------------- 3 files changed, 5 insertions(+), 25 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b707954..cd0fb04 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -169,7 +169,7 @@ process { publishDir = [ path: { "${params.outdir}/minimap2/index" }, mode: params.publish_dir_mode, - enabled: params.save_minimap2_hostremoval_index, + enabled: params.save_hostremoval_index, pattern: 'minimap2' ] } @@ -179,7 +179,7 @@ process { publishDir = [ path: { "${params.outdir}/minimap2/align" }, mode: params.publish_dir_mode, - enabled: params.save_minimap2_hostremoval_mapped, + enabled: params.save_hostremoval_mapped, pattern: '*.bam' ] } @@ -190,7 +190,7 @@ process { publishDir = [ path: { "${params.outdir}/samtools/view" }, mode: params.publish_dir_mode, - enabled: params.save_samtools_unmapped_bam, + enabled: params.save_hostremoval_unmapped, pattern: '*.bam' ] } @@ -200,7 +200,7 @@ process { publishDir = [ path: { "${params.outdir}/samtools/bam2fq" }, mode: params.publish_dir_mode, - enabled: params.save_minimap2_unmapped_fq, + enabled: params.save_hostremoval_unmapped, pattern: '*.fq.gz' ] } diff --git a/nextflow.config b/nextflow.config index 95daba9..8c99af2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -84,14 +84,10 @@ params { perform_shortread_hostremoval = false shortread_hostremoval_reference = null shortread_hostremoval_index = null + longread_hostremoval_index = null save_hostremoval_index = false save_hostremoval_mapped = false save_hostremoval_unmapped = false - longread_hostremoval_index = null - save_minimap2_hostremoval_index = false - save_minimap2_hostremoval_mapped = false - save_samtools_unmapped_bam = false - save_minimap2_unmapped_fq = false // MALT diff --git a/nextflow_schema.json b/nextflow_schema.json index 1902e27..9e4cc6c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -401,22 +401,6 @@ "longread_hostremoval_index": { "type": "string", "default": "None" - }, - "save_minimap2_hostremoval_index": { - "type": "boolean", - "description": "Flag for publishing minimap2 host removal index" - }, - "save_minimap2_hostremoval_mapped": { - "type": "boolean", - "description": "Flag for publishinig bam file with all long reads mapped to a reference" - }, - "save_samtools_unmapped_bam": { - "type": "boolean", - "description": "Flag for publishing bam for reads that did not map to the host reference" - }, - "save_minimap2_unmapped_fq": { - "type": "boolean", - "description": "Flag for publishing fastq files for reads that did not map to the host reference" } } }