diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 9f94a7d39973dbb83fc9914f1938584809c4706f..8ae1b794c004c18d7bd1934d215bc0be8606a5ef 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -26,7 +26,7 @@ getBag: script: - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli --version > version_deriva.txt - - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6 + - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6 - pytest -m getBag artifacts: name: "$CI_JOB_NAME" diff --git a/workflow/conf/replicate_export_config.json b/workflow/conf/Replicate_For_Input_Bag.json similarity index 100% rename from workflow/conf/replicate_export_config.json rename to workflow/conf/Replicate_For_Input_Bag.json diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 540d5bea16082bd40852bb1508a6a47af4b536ff..25f4a24f894c1ace116b181aab689882d79675e3 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -59,7 +59,7 @@ speciesForce = params.speciesForce email = params.email // Define fixed files -replicateExportConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json") +replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json") executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json") if (params.source == "dev") { source = "dev.gudmap.org"