before_script:
- module load python/3.6.4-anaconda
- pip install --user attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 deriva==1.3.0
- module load singularity/3.5.3
- module load nextflow/20.01.0
- ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/
- mkdir -p ~/.deriva
- mkdir -p ~/.bdbag
variables:
refMoVersion: "38.p6.vM22"
refHuVersion: "38.p12.v31"
refERCCVersion: "92"
stages:
- badges
- deploy
- unit
- aggregation
- reference
- integration
- consistency
build_badges:
stage: badges
before_script:
- module load singularity/3.5.3
- chmod +x ./workflow/scripts/get_updated_badge_info.sh
script:
- echo "Building badges"
- singularity run 'docker://gudmaprbk/gudmap-rbk_base:1.0.0' bash ./workflow/scripts/get_updated_badge_info.sh
artifacts:
paths:
- badges/
pages:
stage: deploy
dependencies:
- build_badges
script:
- mkdir -p public/badges
- mv badges/ public/badges/
artifacts:
paths:
- public
getBag:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
- 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 staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
- pytest -m getBag
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_deriva.txt
expire_in: 7 days
getData:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST
- pytest -m getData
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_bdbag.txt
expire_in: 7 days
parseMetadata:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/python3:1.0.0' python3 --version > version_python.txt
- rep=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p repRID)
- exp=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p expRID)
- study=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p studyRID)
- endsMeta=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsMeta)
- endsManual=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p endsManual)
- stranded=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
- spike=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
- species=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
- readLength=$(singularity run 'docker://gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/parse_meta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p readLength)
- echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
- pytest -m parseMetadata
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_python.txt
expire_in: 7 days
inferMetadata:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/rseqc4.0.0:1.0.0' infer_experiment.py --version > version_rseqc.txt
- >
align=$(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://gudmaprbk/rseqc4.0.0:1.0.0' 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 &&
ended=`singularity run 'gudmaprbk/python3:1.0.0' python3 ./workflow/scripts/infer_meta.sh endness Q-Y5F6_1M.se.inferMetadata.log` &&
if [[ ${ended} == "" ]]; then exit 1; fi
- pytest -m inferMetadata
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_rseqc.txt
expire_in: 7 days
trimData:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --version > version_trimgalore.txt
- singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --basename Q-Y5F6_1M.se ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz
- singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --length 35 --paired --basename Q-Y5F6_1M.pe ./test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz
- readLengthSE=$(zcat *_trimmed.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
- readLengthPE=$(zcat *_1.fq.gz | awk '{if(NR%4==2) print length($1)}' | sort -n | awk '{a[NR]=$0}END{print(NR%2==1)?a[int(NR/2)+1]:(a[NR/2]+a[NR/2+1])/2}')
- pytest -m trimData
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_trimgalore.txt
expire_in: 7 days
downsampleData:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/seqtk1.3:1.0.0' 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
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' hisat2 --version > version_hisat2.txt
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools --version > version_samtools.txt
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' 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://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.se.bam Q-Y5F6_1M.se.sam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.bam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.bam Q-Y5F6_1M.se.sorted.bam.bai
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' 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_val_1.fq.gz -2 ./test_data/fastq/small/Q-Y5F6_1M.pe_val_2.fq.gz --summary-file Q-Y5F6_1M.pe.alignSummary.txt --new-summary
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools view -1 -@ 20 -F 4 -F 8 -F 256 -o Q-Y5F6_1M.pe.bam Q-Y5F6_1M.pe.sam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.bam
- singularity run 'docker://gudmaprbk/hisat2.2.1:1.0.0' samtools index -@ 20 -b Q-Y5F6_1M.pe.sorted.bam Q-Y5F6_1M.pe.sorted.bam.bai
- pytest -m alignData
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_hisat2.txt
- version_samtools.txt
expire_in: 7 days
dedupData:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' samtools --version > version_samtools.txt
- singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates --version 2> version_markdups.txt&
- singularity run 'docker://gudmaprbk/picard2.23.9:1.0.0' 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://gudmaprbk/picard2.23.9:1.0.0' 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://gudmaprbk/picard2.23.9:1.0.0' samtools index -@ 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai
- >
for i in {"chr8","chr4","chrY"}; do
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://gudmaprbk/picard2.23.9:1.0.0' parallel -j 20 -k
- pytest -m dedupData
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_markdups.txt
- version_samtools.txt
expire_in: 7 days
countData:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/geneID.tsv
- ln -s /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/Entrez.tsv
- singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' featureCounts -T 20 -a /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.gtf -G /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/genome.fna -g 'gene_name' --extraAttributes 'gene_id' -o Q-Y5F6_1M.se_countData -s 1 -R SAM --primary --ignoreDup ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam
- singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/calculateTPM.R --count ./test_data/counts/small/Q-Y5F6_1M.se_countData
- singularity run 'docker://gudmaprbk/subread2.0.1:1.0.0' Rscript ./workflow/scripts/convertGeneSymbols.R --repRID Q-Y5F6_1M.se
- assignedReads=$(grep -m 1 'Assigned' *.summary | grep -oe '\([0-9.]*\)')
- singularity run 'docker://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: "$CI_JOB_NAME"
when: always
paths:
- version_featurecounts.txt
- version_r.txt
expire_in: 7 days
makeBigWig:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' deeptools --version > version_deeptools.txt
- singularity run 'docker://gudmaprbk/deeptools3.5.0:1.0.0' bamCoverage -p 20 -b ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam -o Q-Y5F6_1M.se.bw
- pytest -m makeBigWig
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- version_deeptools.txt
expire_in: 7 days
fastqc:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- 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: "$CI_JOB_NAME"
when: always
paths:
- version_fastqc.txt
expire_in: 7 days
dataQC:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
- >
for i in {"chr8","chr4","chrY"}; do
echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${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://gudmaprbk/rseqc4.0.0:1.0.0' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
- pytest -m dataQC
uploadInputBag:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > test.txt
- >
md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
size=$(wc -c < ./test.txt) &&
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=${md5}) &&
if [ "${exist}" == "[]" ]; then
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt --parents) &&
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_input_bag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o staging.gudmap.org -c ${cookie}) &&
echo ${rid} test input bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
rid=${rid:8:-6} &&
echo ${rid} test input bag already exists
fi
uploadExecutionRun:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" == "[]" ]; then
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
echo ${rid} test execution run created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
rid=${rid:7:-6} &&
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BTFM -g 17-BT50 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
echo ${rid} test execution run already exists
fi
uploadQC:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
for rid in ${rids}; do
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t mRNA_QC -o staging.gudmap.org -c ${cookie}
done
echo all old mRNA QC RIDs deleted
fi
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BTG4 -p "Single Read" -s forward -l 35 -w 5 -f 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
echo ${rid} test mRNA QC created
uploadProcessedFile:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > 17-BTFJ_test.csv
- mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BTG4/
- mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BTG4/17-BTFJ_test.csv
- >
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
if [ "${exist}" != "[]" ]; then
rids=$(echo ${exist} | grep -o '\"RID\":\".\{7\}' | sed 's/^.\{7\}//') &&
for rid in ${rids}; do
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/delete_entry.py -r ${rid} -t Processed_File -o staging.gudmap.org -c ${cookie}
done
echo all old processed file RIDs deleted
fi
singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-upload-cli --catalog 2 --token ${cookie:9} staging.gudmap.org ./deriva
echo test processed file uploaded
- mkdir test
- singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag test --archiver zip
- echo test output bag created
- pytest -m outputBag
uploadOutputBag:
stage: unit
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
- echo THIS IS A TEST FILE > test.txt
- >
md5=$(md5sum ./test.txt | awk '{ print $1 }') &&
size=$(wc -c < ./test.txt) &&
exist=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Output_Bag/File_MD5=${md5}) &&
if [ "${exist}" == "[]" ]; then
cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
cookie=${cookie:11:-1} &&
loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/upload_output_bag.py -e 17-BTG4 -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
echo ${rid} test output bag created
else
rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
rid=${rid:8:-6} &&
echo ${rid} test output bag already exists
fi
generateVersions:
stage: aggregation
only:
- push
- tags
except:
- merge_requests
script:
- singularity run 'docker://gudmaprbk/multiqc1.9:1.0.0' multiqc --version > version_multiqc.txt
- python ./workflow/scripts/generate_versions.py -o software_versions
- python ./workflow/scripts/generate_references.py -r ./docs/references.md -o software_references
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- software_references_mqc.yaml
- software_versions_mqc.yaml
expire_in: 7 days
human_BioHPC:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- mkdir -p hu
- cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./hu/
mouse_BioHPC:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- mkdir -p mo
- cp -R /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/hisat2 ./mo/
human_dev:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=dev.gudmap.org
- refName=GRCh
- references=$(echo ${referenceBase}/${refName}${refHuVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
mouse_dev:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=dev.gudmap.org
- refName=GRCm
- references=$(echo ${referenceBase}/${refName}${refMoVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
human_staging:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=staging.gudmap.org
- refName=GRCh
- references=$(echo ${referenceBase}/${refName}${refHuVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
mouse_staging:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=staging.gudmap.org
- refName=GRCm
- refHuVersion=38.p6.vM22
- references=$(echo ${referenceBase}/${refName}${refMoVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
human_prod:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=www.gudmap.org
- refName=GRCh
- references=$(echo ${referenceBase}/${refName}${refHuVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
mouse_prod:
stage: reference
only:
- push
- tags
except:
- merge_requests
script:
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- referenceBase=www.gudmap.org
- refName=GRCm
- refHuVersion=38.p6.vM22
- references=$(echo ${referenceBase}/${refName}${refMoVersion})
- GRCv=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f1)
- GRCp=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f2)
- GENCODE=$(echo ${references} | grep -o ${refName}.* | cut -d '.' -f3)
- query=$(echo 'https://'${referenceBase}'/ermrest/catalog/2/entity/RNASeq:Reference_Genome/Reference_Version='${GRCv}'.'${GRCp}'/Annotation_Version=GENCODE%20'${GENCODE})
- curl --request GET ${query} > refQuery.json
- refURL=$(python ./workflow/scripts/extract_ref_data.py --returnParam URL)
- loc=$(dirname ${refURL})
- if [ "${loc}" = "/hatrac/*" ]; then echo "reference not present in hatrac"; exit 1; fi
- filename=$(echo $(basename ${refURL}) | grep -oP '.*(?=:)')
- test=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host ${referenceBase} ls ${loc}/)
- test=$(echo ${test} | grep -o ${filename})
- if [ "${test}" == "" ]; then echo "reference file not present"; exit 1; fi
integration_se:
stage: integration
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 -with-dag dag.png --ci true --email 'venkat.malladi@utsouthwestern.edu,Gervaise.Henry@UTSouthwestern.edu'
- find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- output/qc/
- output/report/
- SE_multiqc_data.json
expire_in: 7 days
retry:
max: 0
when:
- always
integration_pe:
stage: integration
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA -with-dag dag.png --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- dag.png
- output/qc/
- output/report/
- PE_multiqc_data.json
expire_in: 7 days
retry:
max: 0
when:
- always
override_inputBag:
stage: integration
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- inputBagOverride_PE_multiqc_data.json
expire_in: 7 days
retry:
max: 0
when:
- always
override_fastq:
stage: integration
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- fastqOverride_PE_multiqc_data.json
expire_in: 7 days
retry:
max: 0
when:
- always
override_species:
stage: integration
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- hostname
- ulimit -a
- nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --speciesForce 'Homo sapiens' --upload false --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_PE_multiqc_data.json \;
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- speciesOverride_PE_multiqc_data.json
expire_in: 7 days
retry:
max: 0
when:
- always
consistency:
stage: consistency
only: [merge_requests]
except:
variables:
- $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
script:
- pytest -m consistencySE
- pytest -m consistencyPE
artifacts:
name: "$CI_JOB_NAME"
when: always
paths:
- SE_multiqc_data.json
- PE_multiqc_data.json
expire_in: 7 days