Merge pull request #155 from CCBR/fix-sicer

fix: use islands-summary output from sicer
CCBR · Nov 21, 2023 · 1bc3c7f · 1bc3c7f
2 parents 330418d + b6d9ddb
commit 1bc3c7f
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@
   - Input normalized profile plots
   - Protein-coding-only versions of plots
   - Ensure sample IDs are sorted (#150)
+- Fixed a bug where the wrong SICER output file was used for downstream analyses. (#155)
 
 ## CHAMPAGNE 0.2.1
 

diff --git a/modules/local/peaks.nf b/modules/local/peaks.nf
@@ -114,8 +114,8 @@ process SICER {
         tuple val(meta), path(chip), path(input), val(fraglen), val(genome_frac)
 
     output:
-        tuple val(meta), path("*island.bed"), val("${task.process.tokenize(':')[-1].toLowerCase()}"), emit: peak
-        //tuple path("*.scoreisland"), path("*normalized.wig"), path("*islands-summary")
+        tuple val(meta), path("*islands-summary"), val("${task.process.tokenize(':')[-1].toLowerCase()}"), emit: peak
+        tuple path("*island.bed"), path("*.scoreisland"), path("*normalized.wig"),                         emit: sicer
 
     script:
     """

diff --git a/subworkflows/local/peaks.nf b/subworkflows/local/peaks.nf
@@ -91,7 +91,8 @@ workflow CALL_PEAKS {
             ch_peaks = ch_peaks.mix(MACS_NARROW.out.peak)
         }
         if (params.run.sicer) {
-            ch_sicer | SICER | CONVERT_SICER
+            ch_sicer | SICER
+            SICER.out.peak | CONVERT_SICER
             ch_peaks = ch_peaks.mix(CONVERT_SICER.out.peak)
         }
         if (params.run.gem) {