From 435f388902c3b397179a4a979197515ef0828f03 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Nov 2020 20:54:23 -0600
Subject: [PATCH] Update Markdups.
---
.gitlab-ci.yml | 2 +-
workflow/scripts/generate_versions.py | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b0e8d25..e3e052a 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -181,7 +181,7 @@ dedupData:
echo "samtools view -b Q-Y5F6_1M.se.sorted.deduped.bam ${i} > Q-Y5F6_1M.se.sorted.deduped.${i}.bam; samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.${i}.bam Q-Y5F6_1M.se.sorted.deduped.${i}.bam.bai;";
done | singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' parallel -j 20 -k
- pytest -m dedupData
- - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version &> version_markdups.txt
+ - singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates &> version_markdups.txt
- singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools --version > version_samtools.txt
artifacts:
name: "$CI_JOB_NAME"
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 57e5a1f..f3d381b 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -38,13 +38,13 @@ SOFTWARE_REGEX = {
'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
'HISAT2': ['version_hisat.txt', r"/hisat2-2.1.0/hisat2-align-s version (\S+)"],
'Samtools': ['version_samtools.txt', r"samtools (\S+)"],
- 'picard (MarkDuplicates)': ['version_markdups.txt', r"(\S+)"],
+ 'picard (MarkDuplicates)': ['version_markdups.txt', r"Version: (\S+)"],
'featureCounts': ['version_featurecounts.txt', r"featureCounts v(\S+)"],
'R': ['version_r.txt', r"R version (\S+)"],
'deepTools': ['version_deeptools.txt', r"deeptools (\S+)"],
'FastQC': ['version_fastqc.txt', r"FastQC v(\S+)"],
'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
- "Pipeline Version": ['./workflow/nextflow.config', r"version = 'v(\S+)'"]
+ 'Pipeline Version': ['./workflow/nextflow.config', r"version = 'v(\S+)'"]
}
--
GitLab