Add whitelist parameter to kb module

modules/nf-core/kallistobustools/count/main.nf

@@ -13,6 +13,7 @@ process KALLISTOBUSTOOLS_COUNT {
     path  t2g
     path  t1c
     path  t2c
+    path  whitelist
     val   technology
     val   workflow_mode
 
@@ -25,11 +26,12 @@ process KALLISTOBUSTOOLS_COUNT {
     task.ext.when == null || task.ext.when
 
     script:
-    def args    = task.ext.args ?: ''
-    def prefix  = task.ext.prefix ?: "${meta.id}"
-    def cdna    = t1c ? "-c1 $t1c" : ''
-    def intron  = t2c ? "-c2 $t2c" : ''
-    def memory  = task.memory.toGiga() - 1
+    def args      = task.ext.args ?: ''
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def cdna      = t1c ? "-c1 $t1c" : ''
+    def intron    = t2c ? "-c2 $t2c" : ''
+    def whitelist = whitelist ? "-w $whitelist" : ''
+    def memory    = task.memory.toGiga() - 1
     """
     kb \\
         count \\
@@ -38,6 +40,7 @@ process KALLISTOBUSTOOLS_COUNT {
         -g $t2g \\
         $cdna \\
         $intron \\
+        $whitelist \\
         -x $technology \\
         --workflow $workflow_mode \\
         $args \\

modules/nf-core/kallistobustools/count/meta.yml

@@ -42,6 +42,10 @@ input:
         type: file
         description: kb ref's c2 intron_t2c file
         pattern: "*.{intron_t2c.txt}"
+  - - whitelist:
+        type: file
+        description: barcode whitelist file
+        pattern: "*.txt"
   - - technology:
         type: string
         description: String value defining the sequencing technology used.

modules/nf-core/kallistobustools/count/tests/main.nf.test

@@ -41,8 +41,9 @@ nextflow_process {
                 input[2] = KALLISTOBUSTOOLS_REF.out.t2g
                 input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }   // when empty the module doesn't run unless something is passed.
                 input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed.
-                input[5] = "10XV3"
-                input[6] = "standard"
+                input[5] = [] // Barcode whitelist is not required, as 10XV3 is used
+                input[6] = "10XV3"
+                input[7] = "standard"
                 """
             }
         }
@@ -82,8 +83,9 @@ nextflow_process {
                 input[2] = KALLISTOBUSTOOLS_REF.out.t2g
                 input[3] = KALLISTOBUSTOOLS_REF.out.cdna_t2c.ifEmpty{ [] }   // when empty the module doesn't run unless something is passed.
                 input[4] = KALLISTOBUSTOOLS_REF.out.intron_t2c.ifEmpty{ [] } // when empty the module doesn't run unless something is passed.
-                input[5] = "10XV3"
-                input[6] = "standard"
+                input[5] = [] // Barcode whitelist is not required, as 10XV3 is used
+                input[6] = "10XV3"
+                input[7] = "standard"
                 """
             }
         }

modules/nf-core/kallistobustools/count/tests/main.nf.test.snap

@@ -71,10 +71,10 @@
             [
                 "    \"commands\": [",
                 "        \"kallisto bus -i kb_ref_out.idx -o test.count -x 10XV3 -t 2 subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R1_001.fastq.gz subsampled_SC3_v3_NextGem_DI_CellPlex_Human_PBMC_10K_1_gex_S2_L001_R2_001.fastq.gz\",",
-                "        \"bustools sort -o test.count/tmp/output.s.bus -T test.count/tmp -t 2 -m 2G test.count/output.bus\",",
+                "        \"bustools sort -o test.count/tmp/output.s.bus -T test.count/tmp -t 2 -m 3G test.count/output.bus\",",
                 "        \"bustools inspect -o test.count/inspect.json -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",",
                 "        \"bustools correct -o test.count/tmp/output.s.c.bus -w test.count/10x_version3_whitelist.txt test.count/tmp/output.s.bus\",",
-                "        \"bustools sort -o test.count/output.unfiltered.bus -T test.count/tmp -t 2 -m 2G test.count/tmp/output.s.c.bus\",",
+                "        \"bustools sort -o test.count/output.unfiltered.bus -T test.count/tmp -t 2 -m 3G test.count/tmp/output.s.c.bus\",",
                 "        \"bustools count -o test.count/counts_unfiltered/cells_x_genes -g t2g.txt -e test.count/matrix.ec -t test.count/transcripts.txt --genecounts --umi-gene test.count/output.unfiltered.bus\"",
                 "    ],"
             ],
@@ -92,9 +92,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-03-01T15:48:24.476953631"
+        "timestamp": "2025-01-26T19:28:54.613634668"
     }
 }