From 0c3474402e1792c35836da42266db0e77d78e91e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 4 Jan 2021 09:32:59 -0600
Subject: [PATCH] Fix tin by chromosome
---
workflow/rna-seq.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 567c720..e695f5a 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -1248,7 +1248,7 @@ process dedupData {
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 | grep -o chr.* | cut -f3 | sort | uniq`;
+ for i in `samtools view ${repRID}_sorted.deduped.bam | cut -f3 | grep -o chr.[0-9]* | 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"
done | parallel -j `nproc` -k
@@ -1445,7 +1445,7 @@ process dataQC {
# calcualte TIN values per feature on each chromosome
echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > ${repRID}_sorted.deduped.tin.xls
- for i in `cat ./genome.bed | cut -f1 | grep -o chr.* | sort | uniq`; do
+ for i in `cat ./genome.bed | cut -f1 | grep -o chr.[0-9]* | sort | uniq`; do
echo "echo \"LOG: running tin.py on \${i}\" >> ${repRID}.dataQC.log; tin.py -i ${repRID}_sorted.deduped.\${i}.bam -r ./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
@@ -1823,7 +1823,7 @@ process finalizeExecutionRun {
path credential, stageAs: "credential.json" from deriva_finalizeExecutionRun
val executionRunRID from executionRunRID_finalizeExecutionRun
val inputBagRID from inputBagRID_finalizeExecutionRun
- path outputBagRID
+ val outputBagRID
val endsMeta from endsMeta_finalizeExecutionRun
val strandedMeta from strandedMeta_finalizeExecutionRun
val spikeMeta from spikeMeta_finalizeExecutionRun
--
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