diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b63a579db18544ff7625bfd22adae3f218460703..0e24cc0d6d4eeec84f74929b615f8b4fa1b6f7ba 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -50,7 +50,7 @@ getData: - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bdbag --version > version_bdbag.txt - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt - unzip ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip - - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag_20201228 Q-Y5F6 TEST + - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6_inputBag Q-Y5F6 TEST - pytest -m getData artifacts: name: "$CI_JOB_NAME" diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 30f9bd126b7ec602381de244a1eab301845e8e84..00b8c9636acb0851d6f695f9271e7162dc36db5e 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -241,7 +241,7 @@ process getData { # bag fetch fastq's only and rename by repRID echo -e "LOG: fetching replicate bdbag" >> ${repRID}.getData.log - sh ${script_bdbagFetch} \${replicate} ${repRID} + sh ${script_bdbagFetch} \${replicate::-9} ${repRID} echo -e "LOG: fetched" >> ${repRID}.getData.log """ }