Update Markdups.

.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"

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+)'"]
 }