refactor cnvkit logic

nf-core · Sep 6, 2023 · 7afbbec · 7afbbec
1 parent 44cffd6
commit 7afbbec
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Showing 2 changed files with 19 additions and 8 deletions.
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -10,6 +10,7 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
+                "meta": ["id"],
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },
             "bam": {

diff --git a/workflows/createpanelrefs.nf b/workflows/createpanelrefs.nf
@@ -38,15 +38,11 @@ for (param in checkPathParamList) if (param) file(param, checkIfExists: true)
 ch_from_samplesheet = Channel.fromSamplesheet("input")
 
 ch_input = ch_from_samplesheet.map{meta, bam, bai, cram, crai ->
-    if (bam)  return [ [id:"panel", data_type:"bam"  ], bam ]
-    if (cram) return [ [id:"panel", data_type:"cram" ], cram ]
-}.groupTuple().branch{
-    bam:  it[0].data_type == "bam"
-    cram: it[0].data_type == "cram"
+    if (bam)  return [ meta + [data_type:"bam"], bam ]
+    if (cram) return [ meta + [data_type:"cram" ], cram ]
 }
-
 // Initialize file channels based on params, defined in the params.genomes[params.genome] scope
-ch_fasta = params.fasta ? Channel.fromPath(params.fasta).first() : Channel.empty()
+ch_fasta = params.fasta ? Channel.fromPath(params.fasta).map { fasta -> [[id:fasta.baseName],fasta]}.collect() : Channel.empty()
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -97,7 +93,21 @@ workflow CREATEPANELREFS {
     ch_versions = Channel.empty()
 
     if (params.tools && params.tools.split(',').contains('cnvkit')) {
-        CNVKIT_BATCH ( ch_input.bam.map{meta, bam -> [ meta, [], bam ]}, ch_fasta, [], [], [], true )
+
+        ch_input
+        .map{ meta, bam ->
+            new_meta = meta + [id:"panel"]
+            [new_meta, bam]
+        }
+        .groupTuple()
+        .branch{
+            bam:  it[0].data_type == "bam"
+        }
+        .bam
+        .map {meta, bam -> [ meta, [], bam ]}
+        .set { ch_cnvkit_input }
+
+        CNVKIT_BATCH ( ch_cnvkit_input, ch_fasta, [[:],[]], [[:],[]], [[:],[]], true )
         ch_versions = ch_versions.mix(CNVKIT_BATCH.out.versions)
     }