diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3d1880a074452b9821d2203330f7ef0b2a9ff012..6ca72df77a31b2de9608bb0a426a46bb6695fc0c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -655,7 +655,7 @@ override_inputBag: 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.zip --upload false --ci true + - 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" diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh index 345d4949e3bf6e48207066e91a67e1581b8ac8fe..8f5cebc6180a739189693c62451a3eb0f1970245 100644 --- a/test_data/createTestData.sh +++ b/test_data/createTestData.sh @@ -13,10 +13,10 @@ ln -sfn ./test_data/auth/credential.json ~/.deriva/credential.json mkdir -p ./NEW_test_data/bag 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 -cp Q-Y5F6_inputBag.zip ./NEW_test_data/bag/Q-Y5F6_inputBag.zip +cp Q-Y5F6_inputBag.zip ./NEW_test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip mkdir -p ./NEW_test_data/fastq -unzip ./NEW_test_data/bag/Q-Y5F6_inputBag.zip +unzip ./NEW_test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ../workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 cp Q-Y5F6.R1.fastq.gz ./NEW_test_data/fastq/Q-Y5F6.R1.fastq.gz cp Q-Y5F6.R2.fastq.gz ./NEW_test_data/fastq/Q-Y5F6.R2.fastq.gz