From 40391a80dcc4d2485214268a99434fb73d567829 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 2 Nov 2023 11:53:32 -0600 Subject: [PATCH] made some files optional --- modules/freyja.nf | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/freyja.nf b/modules/freyja.nf index 4f58037..e27bea7 100644 --- a/modules/freyja.nf +++ b/modules/freyja.nf @@ -19,7 +19,7 @@ process freyja_variants { output: tuple val(sample), file("freyja/${sample}_{depths,variants}.tsv"), optional: true, emit: variants - path "freyja/${sample}*", emit: files + path "freyja/${sample}*", optional: true, emit: files path "logs/${task.process}/${sample}.${workflow.sessionId}.log" shell: @@ -60,7 +60,7 @@ process freyja_demix { output: path "freyja/${sample}_demix.tsv", optional: true, emit: demix - path "freyja/${sample}*", emit: files + path "freyja/${sample}*", optional: true, emit: files path "logs/${task.process}/${sample}.${workflow.sessionId}.log" shell: @@ -120,7 +120,6 @@ process freyja_boot { ''' } - process freyja_aggregate { tag "Aggregating results from freyja" label "process_single" @@ -144,7 +143,7 @@ process freyja_aggregate { output: path "freyja/aggregated*", emit: files path "freyja/aggregated-freyja.tsv", emit: aggregated_freyja_file - path "freyja/*mqc.png", emit: for_multiqc + path "freyja/*mqc.png", emit: for_multiqc path "freyja/*png" path "logs/${task.process}/${task.process}.${workflow.sessionId}.log"