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Commit 67b0e41e authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Move fastqc before trim

parent 1f07208d
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2 merge requests!65Develop,!64Resolve "samtools sort: couldn't allocate memory for bam_mem"
......@@ -284,12 +284,12 @@ if (fastqsForce != "") {
.ifEmpty { exit 1, "override inputBag file not found: ${fastqsForce}" }
.collect().into {
fastqs_parseMetadata
fastqs_trimData
fastqs_fastqc
}
} else {
fastqs.into {
fastqs_parseMetadata
fastqs_trimData
fastqs_fastqc
}
}
......@@ -542,7 +542,6 @@ process trimData {
output:
path ("*.fq.gz") into fastqsTrim
path ("*.fastq.gz", includeInputs:true) into fastqs_fastqc
path ("*_trimming_report.txt") into trimQC
path ("readLength.csv") into readLengthInfer_fl
......@@ -1659,17 +1658,16 @@ process fastqc {
path (fastq) from fastqs_fastqc
val fastqCountError_fastqc
val fastqReadError_fastqc
val speciesError_fastqc
val pipelineError_fastqc
output:
path ("*.fastq.gz", includeInputs:true) into fastqs_trimData
path ("*_fastqc.zip") into fastqc
path ("rawReads.csv") into rawReadsInfer_fl
when:
fastqCountError_fastqc == 'false'
fastqReadError_fastqc == 'false'
speciesError_fastqc == 'false'
pipelineError_fastqc == 'false'
script:
......
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