Add new docker images to CI

.gitlab-ci.yml

@@ -15,7 +15,7 @@ getBag:
   stage: unit
   script:
   - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
   - pytest -m getBag
 
 getData:
@@ -23,20 +23,20 @@ getData:
   script:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bagit/Replicate_Q-Y5F6.zip
-  - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST
   - pytest -m getData
 
 parseMetadata:
   stage: unit
   script:
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike
-  - singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike
+  - singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species
 
 inferMetadata:
   stage: unit
@@ -45,7 +45,7 @@ inferMetadata:
     align=$(echo $(grep "Overall alignment rate" ./test_data/meta/Q-Y5F6_1M.se.alignSummary.txt | cut -f2 -d ':' | cut -f2 -d ' ' | tr -d '%')) &&
     if [[ ${align} == "" ]]; then exit 1; fi
   - >
-    singularity run 'docker://bicf/rseqc3.0:2.0.0' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
+    singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' infer_experiment.py -r "/project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed" -i "./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam" 1>> Q-Y5F6_1M.se.inferMetadata.log &&
     ended=`singularity run 'docker://bicf/python3:1.3' python3 ./workflow/scripts/inferMeta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
     if [[ ${ended} == "" ]]; then exit 1; fi
   - pytest -m inferMetadata
@@ -68,20 +68,20 @@ trimData:
 downsampleData:
   stage: unit
   script:
-  - singularity exec 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz 1000 1> sampled.1.fq
+  - 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
 
 alignData:
   stage: unit
   script:
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_R2_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
-  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.se.unal.gz -S Q-Y5F6_1M.se.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness F -U ./test_data/fastq/small/Q-Y5F6_1M.se_trimmed.fq.gz --summary-file Q-Y5F6_1M.se.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' hisat2 -p 20 --add-chrname --un-gz Q-Y5F6_1M.pe.unal.gz -S Q-Y5F6_1M.pe.sam -x /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2/genome --rna-strandness FR --no-mixed --no-discordant -1 ./test_data/fastq/small/Q-Y5F6_1M.pe_R1_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_R2_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
+  - singularity run 'docker://bicf/gudmaprbkaligner:2.0.1_indev' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
   - pytest -m alignData
 
 dedupData:
@@ -106,13 +106,13 @@ countData:
 makeBigWig:
   stage: unit
   script:
-  - singularity run 'docker://bicf/deeptools3.3:2.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
+  - 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
   - pytest -m makeBigWig
 
 fastqc:
   stage: unit
   script:
-  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
+  - singularity run 'docker://bicf/fastqc:2.0.1_indev' ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -o .
   - pytest -m fastqc
 
 dataQC:
@@ -120,7 +120,7 @@ dataQC:
   script:
   - echo -e  "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - for i in {"chr8","chr4","chrY"}; do
-    echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
+    echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - pytest -m dataQC
 
 

.gitlab/merge_request_templates/Merge_Request.md

@@ -9,10 +9,11 @@ These are the most common things requested on pull requests.
  - [ ] `CHANGELOG.md` is updated
  - [ ] `README.md` is updated
  - [ ] `LICENSE.md` is updated with new contributors
+ - [ ] Docker images moved to production release and canged in pipeline (including CI)
 
 
 * [ ] **Close issue**\
 Closes #
 
 /cc @ghenry @venkat.malladi
-/assign @ghenry
\ No newline at end of file
+/assign @ghenry