From da95927af060fd7941997ca3d3967f8c223600ae Mon Sep 17 00:00:00 2001 From: Erin Young Date: Fri, 17 May 2024 15:00:20 -0600 Subject: [PATCH] added reads to emit --- modules/local/spades.nf | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/modules/local/spades.nf b/modules/local/spades.nf index 74e58ef..e42a40d 100644 --- a/modules/local/spades.nf +++ b/modules/local/spades.nf @@ -1,7 +1,9 @@ process spades { tag "${meta.id}" label "process_high" - publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + publishDir path: params.outdir, mode: 'copy', pattern: 'logs/*/*log' + publishDir path: params.outdir, mode: 'copy', pattern: 'spades/*' + publishDir path: params.outdir, mode: 'copy', pattern: 'spades/*/*' container 'staphb/spades:3.15.5' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '5h' @@ -10,10 +12,11 @@ process spades { tuple val(meta), file(reads) output: - path "spades/*/*", emit: files + path "spades/*/*", emit: files tuple val(meta), file("contigs/*_contigs.fa"), optional: true, emit: contigs - path "logs/${task.process}/*.log", emit: log - path "versions.yml", emit: versions + tuple val(meta), file("contigs/*_contigs.fa"), file(reads), optional: true, emit: reads_contigs + path "logs/${task.process}/*.log", emit: log + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when