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Commit 4ada2322 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add singularity cache to all nextflow runs

parent 1383fb10
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2 merge requests!76Develop,!71Seqwho
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.gitlab-ci.yml
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......@@ -695,7 +695,7 @@ integration_se:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
- pytest -m completionMultiqc --filename SE_multiqc_data.json
artifacts:
......@@ -720,7 +720,7 @@ integration_pe:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
- pytest -m completionMultiqc --filename PE_multiqc_data.json
artifacts:
......@@ -747,7 +747,7 @@ failAmbiguousSpecies:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ER --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failAmbiguousSpecies_report.html
retry:
max: 0
when:
......@@ -762,7 +762,7 @@ failTrunkation:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
retry:
max: 0
when:
......@@ -777,7 +777,7 @@ failMismatchR1R2:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
retry:
max: 0
when:
......@@ -792,7 +792,7 @@ failUnexpectedMeta:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
retry:
max: 0
when:
......@@ -807,7 +807,7 @@ failFileStructure:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
retry:
max: 0
when:
......@@ -822,7 +822,7 @@ failSeqType:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNDJ --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failSeqType_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNDJ --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failSeqType_report.html
retry:
max: 0
when:
......@@ -837,7 +837,7 @@ override_inputBag:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
- find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./inputBagOverride_multiqc.html \;
- pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
......@@ -862,7 +862,7 @@ override_fastq:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
- find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./fastqOverride_multiqc.html \;
- pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
......@@ -887,7 +887,7 @@ override_species:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
- find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
- pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
......@@ -912,7 +912,7 @@ override_stranded:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
- find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./strandedOverride_multiqc.html \;
- pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
......@@ -937,7 +937,7 @@ override_spike:
script:
- hostname
- ulimit -a
- nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
- export SINGULARITY_CACHEDIR=/project/BICF/BICF_Core/shared/gudmap/singularity_cache/ && nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
- find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
- find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
- pytest -m completionMultiqc --filename spikeOverride_multiqc_data.json
......
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