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GUDMAP_RBK
RNA-seq
Commits
67b0e41e
Commit
67b0e41e
authored
4 years ago
by
Gervaise Henry
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Move fastqc before trim
parent
1f07208d
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!65
Develop
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!64
Resolve "samtools sort: couldn't allocate memory for bam_mem"
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workflow/rna-seq.nf
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67b0e41e
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@@ -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
...
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@@ -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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