From a6562099e16d6c37741123b3ea4f48158db71f87 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 17 Dec 2020 10:55:49 -0600
Subject: [PATCH] Change processed file ouputs to use _ as separator for custom
txt
---
workflow/rna-seq.nf | 28 ++++++++++++++--------------
workflow/scripts/calculateTPM.R | 2 +-
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index d875803..67dfe6e 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -939,8 +939,8 @@ process dedupData {
tuple path (bam), path (bai) from rawBam_dedupData
output:
- tuple path ("${repRID}.sorted.deduped.bam"), path ("${repRID}.sorted.deduped.bam.bai") into dedupBam
- tuple path ("${repRID}.sorted.deduped.*.bam"), path ("${repRID}.sorted.deduped.*.bam.bai") into dedupChrBam
+ tuple path ("${repRID}_sorted.deduped.bam"), path ("${repRID}_sorted.deduped.bam.bai") into dedupBam
+ tuple path ("${repRID}_sorted.deduped.*.bam"), path ("${repRID}_sorted.deduped.*.bam.bai") into dedupChrBam
path ("*.deduped.Metrics.txt") into dedupQC
script:
@@ -955,16 +955,16 @@ process dedupData {
# sort the bam file using Samtools
echo -e "LOG: sorting the bam file" >> ${repRID}.dedup.log
- samtools sort -@ `nproc` -O BAM -o ${repRID}.sorted.deduped.bam ${repRID}.deduped.bam
+ samtools sort -@ `nproc` -O BAM -o ${repRID}_sorted.deduped.bam ${repRID}.deduped.bam
# index the sorted bam using Samtools
echo -e "LOG: indexing sorted bam file" >> ${repRID}.dedup.log
- samtools index -@ `nproc` -b ${repRID}.sorted.deduped.bam ${repRID}.sorted.deduped.bam.bai
+ samtools index -@ `nproc` -b ${repRID}_sorted.deduped.bam ${repRID}_sorted.deduped.bam.bai
# split the deduped BAM file for multi-threaded tin calculation
- for i in `samtools view ${repRID}.sorted.deduped.bam | cut -f3 | sort | uniq`;
+ for i in `samtools view ${repRID}_sorted.deduped.bam | cut -f3 | sort | uniq`;
do
- echo "echo \"LOG: splitting each chromosome into its own BAM and BAI files with Samtools\"; samtools view -b ${repRID}.sorted.deduped.bam \${i} 1>> ${repRID}.sorted.deduped.\${i}.bam; samtools index -@ `nproc` -b ${repRID}.sorted.deduped.\${i}.bam ${repRID}.sorted.deduped.\${i}.bam.bai"
+ echo "echo \"LOG: splitting each chromosome into its own BAM and BAI files with Samtools\"; samtools view -b ${repRID}_sorted.deduped.bam \${i} 1>> ${repRID}_sorted.deduped.\${i}.bam; samtools index -@ `nproc` -b ${repRID}_sorted.deduped.\${i}.bam ${repRID}_sorted.deduped.\${i}.bam.bai"
done | parallel -j `nproc` -k
"""
}
@@ -997,7 +997,7 @@ process makeBigWig {
# create bigwig
echo -e "LOG: creating bibWig" >> ${repRID}.makeBigWig.log
- bamCoverage -p `nproc` -b ${bam} -o ${repRID}.bw
+ bamCoverage -p `nproc` -b ${bam} -o ${repRID}_sorted.deduped.bw
echo -e "LOG: created" >> ${repRID}.makeBigWig.log
"""
}
@@ -1007,7 +1007,7 @@ process makeBigWig {
*/
process countData {
tag "${repRID}"
- publishDir "${outDir}/count", mode: 'copy', pattern: "${repRID}*.tpmTable.csv"
+ publishDir "${outDir}/count", mode: 'copy', pattern: "${repRID}*_tpmTable.csv"
input:
path script_calculateTPM
@@ -1018,7 +1018,7 @@ process countData {
val stranded from strandedInfer_countData
output:
- path ("*.tpmTable.csv") into counts
+ path ("*_tpmTable.csv") into counts
path ("*.countData.summary") into countsQC
path ("assignedReads.csv") into assignedReadsInfer_fl
@@ -1047,10 +1047,10 @@ process countData {
echo -e "LOG: counting ${ends} features" >> ${repRID}.countData.log
if [ "${ends}" == "se" ]
then
- featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o ${repRID}.countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
+ featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o ${repRID}_countData -s \${stranding} -R SAM --primary --ignoreDup ${repRID}_sorted.deduped.bam
elif [ "${ends}" == "pe" ]
then
- featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o ${repRID}.countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}.sorted.deduped.bam
+ featureCounts -T `nproc` -a ./genome.gtf -G ./genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o ${repRID}_countData -s \${stranding} -p -B -R SAM --primary --ignoreDup ${repRID}_sorted.deduped.bam
fi
echo -e "LOG: counted" >> ${repRID}.countData.log
@@ -1142,10 +1142,10 @@ process dataQC {
ulimit -a >> ${repRID}.dataQC.log
# calcualte TIN values per feature on each chromosome
- echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > ${repRID}.sorted.deduped.tin.xls
+ echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > ${repRID}_sorted.deduped.tin.xls
for i in `cat ./bed/genome.bed | cut -f1 | sort | uniq`; do
- echo "echo \"LOG: running tin.py on \${i}\" >> ${repRID}.dataQC.log; tin.py -i ${repRID}.sorted.deduped.\${i}.bam -r ./bed/genome.bed; cat ${repRID}.sorted.deduped.\${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \\\"\\\\t\${i}\\\\t\\\";";
- done | parallel -j `nproc` -k 1>> ${repRID}.sorted.deduped.tin.xls
+ echo "echo \"LOG: running tin.py on \${i}\" >> ${repRID}.dataQC.log; tin.py -i ${repRID}_sorted.deduped.\${i}.bam -r ./bed/genome.bed; cat ${repRID}_sorted.deduped.\${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \\\"\\\\t\${i}\\\\t\\\";";
+ done | parallel -j `nproc` -k 1>> ${repRID}_sorted.deduped.tin.xls
# bin TIN values
echo -e "LOG: binning TINs" >> ${repRID}.dataQC.log
diff --git a/workflow/scripts/calculateTPM.R b/workflow/scripts/calculateTPM.R
index a26bf94..9a163c4 100644
--- a/workflow/scripts/calculateTPM.R
+++ b/workflow/scripts/calculateTPM.R
@@ -30,4 +30,4 @@ tpm <- rpk/scale
output <- cbind(count,tpm)
colnames(output)[7] <- "count"
-write.table(output,file=paste0(repRID,".countTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
+write.table(output,file=paste0(repRID,"_countTable.csv"),sep=",",row.names=FALSE,quote=FALSE)
--
GitLab