Commit 369238e8 authored by Jeremy Mathews's avatar Jeremy Mathews

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
parent 234ba95d
Pipeline #8287 passed with stages
in 5 minutes and 20 seconds
......@@ -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'
......
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