diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1a97d098cdd6545dd913b06b60f40e3fae65e30d..2bf89a8d5c454ed72f2df64c24caa314afc74122 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -303,7 +303,7 @@ uploadInputBag: cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/input_bag/TEST/test.txt) && - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadInputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test input bag' -o dev.gudmap.org -c ${cookie}) && echo ${rid} test input bag created else rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') && @@ -325,12 +325,12 @@ uploadExecutionRun: cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && if [ "${exist}" == "[]" ]; then - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Error -d 'Run in process' -o dev.gudmap.org -c ${cookie} -u F) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Success -d 'This is a test execution run' -o dev.gudmap.org -c ${cookie} -u F) && echo ${rid} test execution run created else rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') && rid=${rid:7:-6} && - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Error -d 'Run in process' -o dev.gudmap.org -c ${cookie} -u ${rid}) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadExecutionRun.py -r 18-MJ3A -w 18-DT5T -g 17-BPD4 -i 18-MHWC -s Success -d 'This is a test execution run' -o dev.gudmap.org -c ${cookie} -u ${rid}) && echo ${rid} test execution run already exists fi @@ -348,12 +348,12 @@ uploadQC: cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && if [ "${exist}" == "[]" ]; then - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -o dev.gudmap.org -c ${cookie} -u F) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o dev.gudmap.org -c ${cookie} -u F) && echo ${rid} test execution run created else rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') && rid=${rid:7:-6} && - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -o dev.gudmap.org -c ${cookie} -u ${rid}) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadQC.py -r 18-MJ3A -e 18-MJ3C -p "Single Read" -s forward -l 35 -w 5 -f 1 -n 'This is a test mRNA QC' -o dev.gudmap.org -c ${cookie} -u ${rid}) && echo ${rid} test execution run already exists fi @@ -382,7 +382,7 @@ uploadOutputBag: cookie=$(cat credential.json | grep -A 1 '\"dev.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') && cookie=${cookie:11:-1} && loc=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' deriva-hatrac-cli --host dev.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt) && - rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -f test.txt -l ${loc} -s ${md5} -b ${size} -o dev.gudmap.org -c ${cookie}) && + rid=$(singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' python3 ./workflow/scripts/uploadOutputBag.py -e -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o dev.gudmap.org -c ${cookie}) && echo ${rid} test output bag created else rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&