Change patterns and changelong.

.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

CHANGELOG.md

 # 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

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+)"],