From acc08c89448cc101cbf0c55a43a809eff7ce4522 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Nov 2020 21:29:38 -0600
Subject: [PATCH] Change patterns and changelong.
---
.gitlab-ci.yml | 4 ++--
CHANGELOG.md | 1 +
workflow/scripts/generate_versions.py | 2 +-
3 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8293fc6..6783133 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -174,7 +174,7 @@ dedupData:
- merge_requests
script:
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools --version > version_samtools.txt
- - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version &> version_markdups.txt; if [ $? -eq 1 ]; then (exit 0); fi
+ - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam ./test_data/bam/small/Q-Y5F6_1M.se.deduped.bam
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
@@ -201,7 +201,7 @@ countData:
script:
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
- - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -v > version_featurecounts.txt
+ - singularity run 'docker://bicf/subread2:2.0.0' featureCounts -v &> version_featurecounts.txt
- singularity run 'docker://bicf/subread2:2.0.0' R --version > version_r.txt
- singularity run 'docker://bicf/subread2:2.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se.countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
- singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 21e5331..0ee5fb6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
# v0.0.4 (in development)
**User Facing**
* Add option to pull references from datahub
+* Add versions and paper references of software used to report
**Background**
* Remove (comment out) option to pull references from S3
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index f3d381b..3fb244f 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -36,7 +36,7 @@ SOFTWARE_REGEX = {
'BDBag': ['version_bdbag.txt', r"BDBag (\S+) \(Bagit \S+\)"],
'RSeQC': ['version_rseqc.txt', r"infer_experiment.py (\S+)"],
'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
- 'HISAT2': ['version_hisat.txt', r"/hisat2-2.1.0/hisat2-align-s version (\S+)"],
+ 'HISAT2': ['version_hisat.txt', r".* version (\S+)"],
'Samtools': ['version_samtools.txt', r"samtools (\S+)"],
'picard (MarkDuplicates)': ['version_markdups.txt', r"Version: (\S+)"],
'featureCounts': ['version_featurecounts.txt', r"featureCounts v(\S+)"],
--
GitLab