From e7d917ee29fb472e5b93c176de739dc41c597640 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sun, 3 Jan 2021 22:43:45 -0600
Subject: [PATCH] Update changelog
---
CHANGELOG.md | 7 +++++++
workflow/rna-seq.nf | 2 +-
2 files changed, 8 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b3749c..6ce68e8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,11 @@
* Upload mRNA QC
* Create and upload output bag
* Add optional to not upload
+* Update references to use bags
+* Update to newer references (GRCh38.p13.v36 and GRCm38.p6.vM25)
+* Use production server for data-hub reference call
+* Stop pipeline if submitted does not match infered
+* Update execution run with "Success" or "Error"
**Background**
* Remove (comment out) option to pull references from S3
@@ -17,10 +22,12 @@
* Changed order of steps so that fastqc is done after the trim step
* Change docker images to production
* Add automated version badges
+* Only calculate/report tin values on regular chromosomes (from gtf)
*Known Bugs*
* Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production
* Override params (inputBag, fastq, species) aren't checked for integrity
+*
<hr>
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 5c548b2..567c720 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 | cut -f3 | sort | uniq`;
+ for i in `samtools view ${repRID}_sorted.deduped.bam | grep -o chr.* | 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"
done | parallel -j `nproc` -k
--
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