From e0a8af869324765ec0c6a375703bfa68f5ba4e77 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Thu, 28 Apr 2022 13:42:14 +0200
Subject: [PATCH] fix outputs

---
 subworkflows/nf-core/bam_qc_picard/main.nf  | 14 ++++++++------
 subworkflows/nf-core/bam_qc_picard/meta.yml |  8 ++------
 2 files changed, 10 insertions(+), 12 deletions(-)

diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
index 747d5995..13f4a845 100644
--- a/subworkflows/nf-core/bam_qc_picard/main.nf
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -8,7 +8,7 @@ include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecth
 
 workflow BAM_QC_PICARD {
     take:
-    ch_bam_bai          // channel: [ val(meta), [ bam ], [bai/csi] ]
+    ch_bam              // channel: [ val(meta), [ bam ]]
     ch_fasta            // channel: [ fasta ]
     ch_bait_interval    // channel: [ bait_interval ]
     ch_target_interval  // channel: [ target_interval ]
@@ -16,7 +16,7 @@ workflow BAM_QC_PICARD {
     main:
     ch_versions = Channel.empty()
 
-    PICARD_COLLECTMULTIPLEMETRICS( ch_bam_bai, ch_fasta )
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
     ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
     if (ch_bait_interval || ch_target_interval) {
         if (ch_bait_interval.isEmpty()) {
@@ -25,16 +25,18 @@ workflow BAM_QC_PICARD {
         if (ch_target_interval.isEmpty()) {
             log.error("Target interval channel is empty")
         }
-        PICARD_COLLECTHSMETRICS( ch_bam_bai, ch_fasta, ch_bait_interval, ch_target_interval )
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_bait_interval, ch_target_interval )
         ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
     } else {
-        PICARD_COLLECTWGSMETRICS( ch_bam_bai, ch_fasta )
+        PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
         ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
     }
 
+    ch_coverage_metrics = Channel.empty()
+    ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.coverage_metrics.first(), PICARD_COLLECTWGSMETRICS.out.coverage_metrics.first())
+
     emit:
-    hs_metrics          = PICARD_COLLECTHSMETRICS.out.hs_metrics    // channel: [ val(meta), [ hs_metrics ] ]
-    wgs_metrics         = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ wgs_metrics ] ]
+    coverage_metrics    = PICARD_COLLECTWGSMETRICS.out.metrics      // channel: [ val(meta), [ coverage_metrics ] ]
     multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
 
     versions = ch_versions                                          // channel: [ versions.yml ]
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
index c4422150..67d3496e 100644
--- a/subworkflows/nf-core/bam_qc_picard/meta.yml
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -44,14 +44,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - hs_metrics:
+  - coverage_metrics:
       type: file
-      description: Alignment metrics files generated by picard CollectHsMetrics
+      description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
       pattern: "*_metrics.txt"
-  - wgs_metrics:
-      type: file
-      description: Alignment metrics files generated by picard CollectWgsMetrics
-      pattern: "*_{metrics}"
   - multiple_metrics:
       type: file
       description: Alignment metrics files generated by picard CollectMultipleMetrics