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Commit 331ce5b8 authored by Jeremy Mathews's avatar Jeremy Mathews
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Fixed RID

parent 89af5024
2 merge requests!58Develop,!51Add run details to output bag
Pipeline #8387 canceled with stages
in 2 minutes and 32 seconds
...@@ -43,7 +43,7 @@ getData: ...@@ -43,7 +43,7 @@ getData:
script: script:
- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag --version > version_bdbag.txt - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag --version > version_bdbag.txt
- ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
- unzip ./test_data/bag/staging/Replicate_Q-Y5F6.zip - unzip ./test_data/bag/staging/Replicate_Q-Y5JA.zip
- singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' 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 - pytest -m getData
artifacts: artifacts:
...@@ -432,7 +432,7 @@ override_inputBag: ...@@ -432,7 +432,7 @@ override_inputBag:
script: script:
- hostname - hostname
- ulimit -a - 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/staging/Replicate_Q-Y5F6.zip --ci true - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --inputBagForce ./test_data/bag/staging/Replicate_Q-Y5JA.zip --ci true
- find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \; - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \;
artifacts: artifacts:
name: "$CI_JOB_NAME" name: "$CI_JOB_NAME"
......
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