fix: broken stuff after module upgrades

brickmanlab · Aug 2, 2024 · 2ef0d66 · 2ef0d66
1 parent ff29455
commit 2ef0d66
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/subworkflows/local/starsolo.nf b/subworkflows/local/starsolo.nf
@@ -10,7 +10,11 @@ workflow STARSOLO {
 
     ch_versions = Channel.empty()
 
-    STARSOLO_ALIGN ( reads, index )
+    STARSOLO_ALIGN (
+        reads,
+        Channel.fromPath("$projectDir/assets/whitelist.tsv", checkIfExists: true),
+        index
+    )
 
     ch_versions = ch_versions.mix(STARSOLO_ALIGN.out.versions.first())
 

diff --git a/workflows/primeseq.nf b/workflows/primeseq.nf
@@ -48,19 +48,14 @@ workflow PRIMESEQ {
             [
                 id: meta.id,
                 plate_id: meta.plate_id,
-                whitelist: ,
                 umi_len: 16,
                 umi_start: 13,
                 cb_len: 12,
                 cb_start: 1,
             ], "CB_UMI_Simple", fastq
         ]
     }
-    STARSOLO (
-        ch_reads,
-        file("$projectDir/assets/whitelist.tsv", checkIfExists: true),
-        ch_star_index
-    )
+    STARSOLO ( ch_reads, ch_star_index )
     ch_versions = ch_versions.mix(STARSOLO.out.versions.first())
     ch_multiqc_files = ch_multiqc_files.mix(STARSOLO.out.for_multiqc)
 
@@ -117,7 +112,9 @@ workflow PRIMESEQ {
         ch_multiqc_files.collect(),
         ch_multiqc_config.toList(),
         ch_multiqc_custom_config.toList(),
-        ch_multiqc_logo.toList()
+        ch_multiqc_logo.toList(),
+        false,
+        false
     )
 
     emit: