remove seqtk and update output for stdout.

.gitlab-ci.yml

@@ -133,15 +133,9 @@ downsampleData:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://bicf/seqtk:2.0.1_indev' seqtk > version_seqtk.txt
   - singularity run 'docker://bicf/seqtk:2.0.1_indev' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
   - pytest -m downsampleData
-  artifacts:
-    name: "$CI_JOB_NAME"
-    when: always
-    paths:
-      - version_seqtk.txt
-    expire_in: 7 days
+
 
 alignData:
   stage: unit
@@ -179,7 +173,7 @@ dedupData:
   except:
     - merge_requests
   script:
-  - 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 &> version_markdups.txt
   - 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 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

docs/references.md

@@ -15,34 +15,31 @@
 5. **trimgalore**:
   * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
 
-6. **seqtk**:
-    * seqtk [https://github.com/lh3/seqtk](https://github.com/lh3/seqtk)
-
-7. **hisat2**:
+6. **hisat2**:
   * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.
 
   Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
 
-8. **samtools**:
+7. **samtools**:
   * Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)
 
-9. **picard**:
+8. **picard**:
   * “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. [http://broadinstitute.github.io/picard/](http://broadinstitute.github.io/picard/); Broad Institute
 
-10. **featureCounts**:
+9. **featureCounts**:
   * Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656).
 
-11. **R**:
+10. **R**:
   * R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:[http://www.R-project.org/](http://www.R-project.org/).
 
-12. **deeptools**:
+11. **deeptools**:
   * Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257)
 
-13. **FastQC**
+12. **FastQC**
   * FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-14. **MultiQC**:
+13. **MultiQC**:
   * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
 
-15. **Nextflow**:
+14. **Nextflow**:
   * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.

workflow/scripts/generate_versions.py

@@ -36,7 +36,6 @@ 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+)"],
-    'seqtk': ['version_seqtk.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+)"],