Merge pull request #77 from grst/fix-kallistobus

Fix kallistobus didn't run with multiple samples
nf-core · Jan 3, 2022 · 63890b7 · 63890b7
2 parents 672864b + 7a784b6
commit 63890b7
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Showing 4 changed files with 16 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * Pipeline ported to dsl2
 * Template update with latest nf-core/tools v2.1
 
+### Fixes
+
+* Make sure pipeline runs on multiple samples [#77](https://github.com/nf-core/scrnaseq/pull/77)
+
 ## v1.1.0 - 2021-03-24 "Olive Mercury Corgi"
 
 * Template update with latest nf-core/tools v1.13.2

diff --git a/workflows/alevin.nf b/workflows/alevin.nf
@@ -173,7 +173,13 @@ workflow SCRNASEQ_ALEVIN {
     /*
     * Perform quantification with salmon alevin
     */
-    SALMON_ALEVIN ( ch_fastq, salmon_index_alevin, ch_txp2gene, protocol, ch_barcode_whitelist )
+    SALMON_ALEVIN (
+        ch_fastq,
+        salmon_index_alevin.collect(),
+        ch_txp2gene.collect(),
+        protocol,
+        ch_barcode_whitelist.collect()
+    )
     ch_software_versions = ch_software_versions.mix(SALMON_ALEVIN.out.version.first().ifEmpty(null))
     ch_salmon_multiqc = SALMON_ALEVIN.out.alevin_results
 

diff --git a/workflows/kallisto_bustools.nf b/workflows/kallisto_bustools.nf
@@ -137,8 +137,8 @@ workflow KALLISTO_BUSTOOLS {
     */
     KALLISTOBUSTOOLS_COUNT(
         ch_fastq,
-        ch_kallisto_index,
-        ch_kallisto_gene_map,
+        ch_kallisto_index.collect(),
+        ch_kallisto_gene_map.collect(),
         [],
         [],
         false,

diff --git a/workflows/starsolo.nf b/workflows/starsolo.nf
@@ -148,9 +148,9 @@ workflow STARSOLO {
     */
     STAR_ALIGN(
         ch_fastq,
-        star_index,
-        gtf,
-        ch_barcode_whitelist,
+        star_index.collect(),
+        gtf.collect(),
+        ch_barcode_whitelist.collect(),
         protocol
     )
     ch_software_versions = ch_software_versions.mix(STAR_ALIGN.out.version.first().ifEmpty(null))