From c5a0bf5e669a978f9d17e35352c50e59dfb00405 Mon Sep 17 00:00:00 2001
From: tives82 <tiverson@utah.gov>
Date: Wed, 29 Nov 2023 12:19:45 -0700
Subject: [PATCH] Added process names for use in versions.yml

---
 modules/local/irma_abricate_report.nf       | 3 +++
 modules/local/qc_report.nf                  | 1 +
 subworkflows/local/preprocessing_read_qc.nf | 1 +
 3 files changed, 5 insertions(+)

diff --git a/modules/local/irma_abricate_report.nf b/modules/local/irma_abricate_report.nf
index 9958bd7..075b6ce 100755
--- a/modules/local/irma_abricate_report.nf
+++ b/modules/local/irma_abricate_report.nf
@@ -12,6 +12,9 @@ process IRMA_ABRICATE_REPORT {
     output:
     tuple val(meta), path("*.combined.typing.tsv"), emit: tsv_combined
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def output_tsv = "${prefix}.combined.typing.tsv"
diff --git a/modules/local/qc_report.nf b/modules/local/qc_report.nf
index 9fe415b..5c79a2d 100755
--- a/modules/local/qc_report.nf
+++ b/modules/local/qc_report.nf
@@ -11,6 +11,7 @@ process QC_REPORT {
 
     output:
     path("*_output.txt"), emit: qc_line
+    path "versions.yml" , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/subworkflows/local/preprocessing_read_qc.nf b/subworkflows/local/preprocessing_read_qc.nf
index aff4096..a3d2b5e 100755
--- a/subworkflows/local/preprocessing_read_qc.nf
+++ b/subworkflows/local/preprocessing_read_qc.nf
@@ -48,6 +48,7 @@ workflow PREPROCESSING_READ_QC {
     ch_qcreport_input = FAQCS.out.txt
     QC_REPORT(ch_qcreport_input)
     ch_qcreport = QC_REPORT.out.qc_line
+    ch_versions = ch_versions.mix(QC_REPORT.out.versions)
 
     if ( !params.skip_kraken2 ) {
         KRAKEN2_KRAKEN2(reads, db, false, true)