Fix wrong container for deriva in ci

.gitlab-ci.yml

@@ -29,8 +29,8 @@ getBag:
     - merge_requests
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-  - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' deriva-download-cli --version > version_deriva.txt
-  - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli --version > version_deriva.txt
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
   - pytest -m getBag
   artifacts:
     name: "$CI_JOB_NAME"
@@ -47,10 +47,10 @@ getData:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bdbag --version > version_bdbag.txt
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bag/staging/Q-Y5F6_inputBag.zip
-  - singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
+  - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST
   - pytest -m getData
   artifacts:
     name: "$CI_JOB_NAME"
@@ -205,12 +205,12 @@ 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 -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
-  - singularity run 'docker://bicf/subread2:2.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
+  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' 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://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se.countData
+  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
   - assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
-  - 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://gudmaprbk/subread2.0.1:1.0.0' featureCounts -v &> version_featurecounts.txt
+  - singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' R --version > version_r.txt
   - pytest -m makeFeatureCounts
   artifacts:
     name: "$CI_JOB_NAME"
@@ -228,8 +228,8 @@ makeBigWig:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://bicf/deeptools3.3:2.0.1_indev' deeptools --version > version_deeptools.txt
-  - singularity run 'docker://bicf/deeptools3.3:2.0.1_indev' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
+  - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
+  - singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
   - pytest -m makeBigWig
   artifacts:
     name: "$CI_JOB_NAME"
@@ -246,8 +246,8 @@ fastqc:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.1_indev' fastqc --version > version_fastqc.txt
-  - singularity run 'docker://bicf/fastqc:2.0.1_indev' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc --version > version_fastqc.txt
+  - singularity run 'docker://gudmaprbk/fastqc0.11.9:1.0.0' fastqc ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
   - pytest -m fastqc
   artifacts:
     name: "$CI_JOB_NAME"
@@ -409,7 +409,7 @@ generateVersions:
   except:
     - merge_requests
   script:
-  - singularity run 'docker://bicf/multiqc1.8:2.0.1_indev' multiqc --version > version_multiqc.txt
+  - singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
   - python ./workflow/scripts/generate_versions.py -o software_versions
   - python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
   artifacts: