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Commit 382be8c7 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Rename fastqs by sample not lane

parent cb957223
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3 merge requests!53Develop,!35Develop,!33Resolve "Change nextflow fastq rename to iterate sample not lane"
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...@@ -188,7 +188,7 @@ process count302 { ...@@ -188,7 +188,7 @@ process count302 {
input: input:
set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples302 set sample, file("${sample}_S?_L001_R1_001.fastq.gz"), file("${sample}_S?_L001_R2_001.fastq.gz") from samples302
file ref from refLocation302.first() file ref from refLocation302.first()
expectCells302 expectCells302
forceCells302 forceCells302
...@@ -217,4 +217,4 @@ process count302 { ...@@ -217,4 +217,4 @@ process count302 {
cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302" cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
""" """
} }
} }
\ No newline at end of file
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