Merge branch 'CW-4181' into 'dev'

demux output channel [CW-4181] Closes CW-4181 See merge request epi2melabs/workflows/wf-basecalling!72
epi2me-labs · Jun 5, 2024 · 7babc4f · 7babc4f
2 parents 65d5cc4 + 6a98cf8
commit 7babc4f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.2.1]
+### Added
+- Output channel for demuxed BAM files for downstream use.
+
 ## [v1.2.0]
 ### Added
 - Support for `dorado demux` to demultiplex barcoded runs. Specify your `--barcode_kit` to activate demultiplexing.

diff --git a/lib/signal/ingress.nf b/lib/signal/ingress.nf
@@ -252,7 +252,7 @@ process split_calls {
     input:
         tuple path(cram), path(crai)
     output:
-        path("demuxed/*")
+        path("demuxed/*.bam")
     shell:
     """
     dorado demux --output-dir demuxed --no-classify ${cram}
@@ -457,12 +457,15 @@ workflow wf_dorado {
             // │   └── reads.bam
             // └── unclassified
             //     └── reads.bam
-            split_calls(pass)
+            barcode_bams = split_calls(pass)
+        } else {
+            barcode_bams = Channel.empty()
         }
 
     emit:
         chunked_pass_crams = crams.pass
         pass = pass
+        barcode_bams = barcode_bams
         fail = fail
         output_exts = output_exts
         summary = summary

diff --git a/nextflow.config b/nextflow.config
@@ -87,7 +87,7 @@ manifest {
     description     = 'Helper workflow for basecalling ONT reads.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = '1.2.0'
+    version         = '1.2.1'
 }
 
 epi2melabs {