fix: issue #3 velocity

nf-core · Jun 26, 2023 · cd91b19 · cd91b19
1 parent 2d3b531
commit cd91b19
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/modules/local/velocity/whitelist/main.nf b/modules/local/velocity/whitelist/main.nf
@@ -11,6 +11,8 @@ process VELOCITY_WHITELIST {
         'biocontainers/mulled-v2-0bcca2890a3ab7be29a83e813a02d340d6f54660:4cb478c6e57df2ef85ea5f8eae6d717c017962cd-0' }"
 
     input:
+    path(amp_batches)
+    path(well_cells)
     tuple val(meta), path(reads)
 
     output:
@@ -24,8 +26,8 @@ process VELOCITY_WHITELIST {
     """
     velocity.py whitelist \\
         --batch $meta.id \\
-        --amp_batches $meta.amp_batches \\
-        --well_cells $meta.well_cells
+        --amp_batches $amp_batches \\
+        --well_cells $well_cells
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/subworkflows/local/velocity.nf b/subworkflows/local/velocity.nf
@@ -9,9 +9,11 @@ include { STAR_ALIGN as VELOCITY_STARSOLO } from '../../modules/nf-core/star/ali
 
 workflow VELOCITY {
     take:
-    reads   // channel [ meta, reads ]
-    index   // channel file(star index)
-    gtf     // channel file(gtf)
+    amp_batches   // channel: amp_batch
+    well_cells    // channel: well_cells
+    reads         // channel [ meta, reads ]
+    index         // channel file(star index)
+    gtf           // channel file(gtf)
 
     main:
     ch_versions = Channel.empty()
@@ -24,7 +26,7 @@ workflow VELOCITY {
     ch_versions = ch_versions.mix(VELOCITY_CONVERT.out.versions)
 
     // build whitelist.txt
-    VELOCITY_WHITELIST ( reads )
+    VELOCITY_WHITELIST ( amp_batches, well_cells, reads )
     ch_versions = ch_versions.mix(VELOCITY_WHITELIST.out.versions)
 
     // trim poly-T and low quality reads

diff --git a/workflows/marsseq.nf b/workflows/marsseq.nf
@@ -153,7 +153,13 @@ workflow MARSSEQ {
     // MODULE: Velocity
     //
     if (params.velocity) {
-        VELOCITY ( PREPARE_PIPELINE.out.reads, ch_star_index, ch_gtf )
+        VELOCITY (
+            INPUT_CHECK.out.reads.map { it[0].amp_batches },
+            INPUT_CHECK.out.reads.map { it[0].well_cells },
+            PREPARE_PIPELINE.out.reads,
+            ch_star_index,
+            ch_gtf
+        )
         ch_versions = ch_versions.mix(VELOCITY.out.versions)
 
         ch_multiqc_files = ch_multiqc_files.mix(VELOCITY.out.catadapt_multiqc.collect{it[1]}.ifEmpty([]))