From 5fc25b2c1e39c3afd2cee3db8d3ccf14b6f08987 Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Wed, 12 Jun 2019 14:18:44 -0500
Subject: [PATCH] Check Input Fastq Files
---
workflow/main.nf | 44 +++++++++++++++++++++++++++++++++++++-------
1 file changed, 37 insertions(+), 7 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index a55b880..3734698 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -3,10 +3,41 @@
// Default parameter values to run tests
params.input = "$baseDir"
params.output= "$baseDir/output"
-params.fastqs="$params.input/*.fastq.gz"
-params.design="$params.input/design.txt"
-params.genome="/project/shared/bicf_workflow_ref/human/GRCh38/"
+params.files="$params.input/*.f*"
+files=Channel.fromPath(params.files)
+
+process checkinputfiles {
+
+ input:
+
+ file fqs from files
+
+ output:
+
+ file("*.fastq.gz") into fastqs
+
+ script:
+
+ """
+ if [[ $fqs == *.fq ]];
+ then new_name=`echo ${fqs} | sed -e "s/.fq\$/.fastq/"`;
+ mv ${fqs} \${new_name};
+ gzip -f \${new_name};
+ elif [[ $fqs == *.fastq ]];
+ then gzip -f $fqs;
+ elif [[ $fqs == *.fq.gz ]];
+ then new_name=`echo ${fqs} | sed -e "s/.fq.gz\$/.fastq.gz/"`;
+ mv ${fqs} \${new_name};
+ else
+ zcat ${fqs} | gzip -c > ${fqs}.temp
+ mv ${fqs}.temp ${fqs}
+ fi;
+ """
+}
+
+params.design="$params.input/design.txt"
+params.genome="/project/shared/bicf_workflow_ref/human/grch38/"
params.markdups="picard"
params.stranded="0"
params.pairs="pe"
@@ -16,14 +47,13 @@ params.fusion = 'skip'
params.dea = 'detect'
design_file = file(params.design)
-fastqs=file(params.fastqs)
design_file = file(params.design)
gtf_file = file("$params.genome/gencode.gtf")
genenames = file("$params.genome/genenames.txt")
geneset = file("$params.genome/../gsea_gmt/$params.geneset")
-dbsnp="$params.genome/dbSnp.vcf.gz"
-indel="$params.genome/GoldIndels.vcf.gz"
+dbsnp="$params.genome/dbsnp.vcf.gz"
+indel="$params.genome/goldindels.vcf.gz"
knownindel=file(indel)
dbsnp=file(dbsnp)
@@ -64,7 +94,7 @@ spltnames
else {
spltnames
.splitCsv()
- .filter { fileMap.get(it[1]) != null }
+ .filter { fleMap.get(it[1]) != null }
.map { it -> tuple(it[0], fileMap.get(it[1]),'') }
.set { read }
}
--
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