diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3a60c64384aadb5de50677736fb18f6866f52d34..213da881fe1e3cf9419aad1db990d091d0202e43 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -43,7 +43,7 @@ getData: script: - 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 - - unzip ./test_data/bag/Replicate_Q-Y5F6.zip + - unzip ./test_data/bag/staging/Replicate_Q-Y5F6.zip - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6 TEST - pytest -m getData artifacts: @@ -432,7 +432,7 @@ 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/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-Y5F6 --inputBagForce ./test_data/bag/staging/Replicate_Q-Y5F6.zip --ci true - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \; artifacts: name: "$CI_JOB_NAME" diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 0a684f07e368d6d6ee132040e9cbf13a5e252b40..1bbf7104be927d96654c739a966225bcf93782cd 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -164,7 +164,7 @@ process getBag { # deriva-download replicate RID echo -e "LOG: fetching bag for ${repRID} in GUDMAP" >> ${repRID}.getBag.log - deriva-download-cli ${source} --catalog 2 ${derivaConfig} . rid=${repRID} + deriva-download-cli staging.gudmap.org --catalog 2 ${derivaConfig} . rid=${repRID} echo -e "LOG: fetched" >> ${repRID}.getBag.log """ }