Fix channels to run for all rangers. Set up for future rangers and new utility...

Fix channels to run for all rangers. Set up for future rangers and new utility belts. Star Command Out

workflow/main.nf

@@ -166,6 +166,11 @@ process untarBCL {
 }
 
 
+versions_bcl2fastqScript.into { versions_bcl2fastqScriptCell; versions_bcl2fastqScriptSpace }
+bclPaths.into { bclPathsCell; bclPathsSpace }
+designPaths.into { designPathsCell; designPathsSpace }
+
+
 process cellranger_mkfastq {
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
@@ -174,17 +179,17 @@ process cellranger_mkfastq {
 
   input:
     file versions_cellrangerScript
-    file versions_bcl2fastqScript
-    each file(bcl) from bclPaths.collect()
-    file design from designPaths
+    file versions_bcl2fastqScriptCell
+    each file(bcl) from bclPathsCell.collect()
+    file design from designPathsCell
 
   output:
-    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPaths
-    val "${bcl.simpleName}" into bclName
-    file("**/outs/**/*.fastq.gz") into rangerCount mode flatten
-    file("**/outs/fastq_path/Stats/*") into bqcPaths
-    file("version_ranger.txt") into version_ranger
-    file("version_bcl2fastq.txt") into version_bcl2fastq
+    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPathsCell
+    val "${bcl.simpleName}" into bclNameCell
+    file("**/outs/**/*.fastq.gz") into cellrangerCount mode flatten
+    file("**/outs/fastq_path/Stats/*") into bqcPathsCell
+    file("version_ranger.txt") into version_cellranger
+    file("version_bcl2fastq.txt") into version_bcl2fastqCell
 
   when:
     ranger == "cellranger"
@@ -212,17 +217,17 @@ process spaceranger_mkfastq {
 
   input:
     file versions_spacerangerScript
-    file versions_bcl2fastqScript
-    each file(bcl) from bclPaths.collect()
-    file design from designPaths
+    file versions_bcl2fastqScriptSpace
+    each file(bcl) from bclPathsSpace.collect()
+    file design from designPathsSpace
 
   output:
-    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPaths
-    val "${bcl.simpleName}" into bclName
-    file("**/outs/**/*.fastq.gz") into rangerCount mode flatten
-    file("**/outs/fastq_path/Stats/*") into bqcPaths
-    file("version_ranger.txt") into version_ranger
-    file("version_bcl2fastq.txt") into version_bcl2fastq
+    file("fq/${bcl.simpleName}/*.fastq.gz") into fastqPathsSpace
+    val "${bcl.simpleName}" into bclNameSpace
+    file("**/outs/**/*.fastq.gz") into spacerangerCount mode flatten
+    file("**/outs/fastq_path/Stats/*") into bqcPathsSpace
+    file("version_ranger.txt") into version_spaceranger
+    file("version_bcl2fastq.txt") into version_bcl2fastqSpace
 
   when:
     ranger == "spaceranger"
@@ -242,6 +247,32 @@ process spaceranger_mkfastq {
 }
 
 
+Channel
+  .empty()
+  .mix(fastqPathsCell,fastqPathsSpace)
+  .set { fastqPaths }
+Channel
+  .empty()
+  .mix(bclNameCell,bclNameSpace)
+  .set { bclName }
+Channel
+  .empty()
+  .mix(cellrangerCount,spacerangerCount)
+  .set { rangerCount }
+Channel
+  .empty()
+  .mix(bqcPathsCell,bqcPathsSpace)
+  .set { bqcPaths }
+Channel
+  .empty()
+  .mix(version_cellranger,version_spaceranger)
+  .set { version_ranger }
+Channel
+  .empty()
+  .mix(version_bcl2fastqCell,version_bcl2fastqSpace)
+  .set { version_bcl2fastq }
+
+
 process fastqc {
   tag "${bcl}"
   module 'fastqc/0.11.5:parallel'