Fix CollectHsMetrics running for only a subset of input samples

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#216](https://github.com/nf-core/seqinspector/pull/216) Fixed meta.id that resulted in all SEQFU_STATS processes with the same tag name
 - [#224](https://github.com/nf-core/seqinspector/pull/224) Fix workflow output syntax for future Nextflow releases
 - [#226](https://github.com/nf-core/seqinspector/pull/226) Fix parameter `tools_bundle` not accepting `null` for custom tool selection
+- Fix `CollectHsMetrics` running for only a subset of input samples by broadcasting bait/target interval channels via `.first()` and forking `ch_bam_bai` with `multiMap` so both `PICARD_COLLECTHSMETRICS` and `PICARD_COLLECTMULTIPLEMETRICS` receive every emission
 
 ### `Changed`
 

subworkflows/local/bam_qc/main.nf

@@ -17,7 +17,20 @@ workflow BAM_QC {
 
     main:
 
-    ch_hsmetrics_in = ch_bam_bai.combine(ch_bait_intervals).combine(ch_target_intervals)
+    // Fork ch_bam_bai into two named branches so both downstream consumers
+    // receive every emission. Without this, the queue channel is
+    // distributed (rather than broadcast) between the .combine() operator
+    // feeding CollectHsMetrics and the direct process input feeding
+    // CollectMultipleMetrics, causing some samples to be silently dropped
+    // from one of the two paths.
+    ch_bam_bai_branched = ch_bam_bai.multiMap { meta, bam, bai ->
+        for_hsmetrics:    tuple(meta, bam, bai)
+        for_multimetrics: tuple(meta, bam, bai)
+    }
+
+    ch_hsmetrics_in = ch_bam_bai_branched.for_hsmetrics
+        .combine(ch_bait_intervals)
+        .combine(ch_target_intervals)
 
     PICARD_COLLECTHSMETRICS(
         ch_hsmetrics_in.filter { ("picard_collecthsmetrics" in tools) },
@@ -28,7 +41,7 @@ workflow BAM_QC {
     )
 
     PICARD_COLLECTMULTIPLEMETRICS(
-        ch_bam_bai.filter { ("picard_collectmultiplemetrics" in tools) },
+        ch_bam_bai_branched.for_multimetrics.filter { ("picard_collectmultiplemetrics" in tools) },
         ch_reference_fasta,
         ch_reference_fai,
     )

workflows/seqinspector.nf

@@ -290,8 +290,8 @@ workflow SEQINSPECTOR {
         bam_bai,
         fasta,
         fai,
-        bait_intervals ? channel.fromPath(bait_intervals).collect() : channel.empty(),
-        target_intervals ? channel.fromPath(target_intervals).collect() : channel.empty(),
+        bait_intervals ? channel.fromPath(bait_intervals).first() : channel.empty(),
+        target_intervals ? channel.fromPath(target_intervals).first() : channel.empty(),
         dict,
         tools,
     )