diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf index a44e6e89a7929485857c29daca30f8e34d7f3048..8b26437596eaaac2f079dd2129b191ba470c079e 100644 --- a/src/nf_modules/fastp/main.nf +++ b/src/nf_modules/fastp/main.nf @@ -6,13 +6,15 @@ process fastp_pairedend { container = "${container_url}" label "big_mem_multi_cpus" tag "$pair_id" + publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html" input: tuple val(pair_id), path(reads) output: tuple val(pair_id), path("*.fastq.gz"), emit: fastq - tuple val(pair_id), path("*.{zip,html,json}"), emit: report + tuple val(pair_id), path("*.html"), emit: html + tuple val(pair_id), path("*.json"), emit: report script: """ @@ -25,7 +27,7 @@ fastp --thread ${task.cpus} \ --out1 ${pair_id}_R1_trim.fastq.gz \ --out2 ${pair_id}_R2_trim.fastq.gz \ --html ${pair_id}.html \ ---json ${pair_id}.json \ +--json ${pair_id}_fastp.json \ --report_title ${pair_id} """ } @@ -34,13 +36,15 @@ process fastp_singleend { container = "${container_url}" label "big_mem_multi_cpus" tag "$pair_id" + publishDir "results/QC/fastp/", mode: 'copy', pattern: "*.html" input: tuple val(pair_id), path(reads) output: tuple val(pair_id), path("*.fastq.gz"), emit: fastq - tuple val(pair_id), path("*.{zip,html,json}"), emit: report + tuple val(pair_id), path("*.html"), emit: html + tuple val(pair_id), path("*.json"), emit: report script: """ @@ -51,7 +55,7 @@ fastp --thread ${task.cpus} \ --in1 ${reads} \ --out1 ${pair_id}_trim.fastq.gz \ --html ${pair_id}.html \ ---json ${pair_id}.json \ +--json ${pair_id}_fastp.json \ --report_title ${pair_id} """ }