diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 3140584c713dde170030e70e9ecf6067d002f9fb..bf959f2d26cff05fa880f399ef151f5061de5e69 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1028,14 +1028,24 @@ dnanexus: - module load dxtoolkit/python27/0.294.0 - export NXF_XPACK_LICENSE=${nxf_license} - dx upload ./test_data/auth/c* --path /ci-env/auth/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} - - dx upload ./test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} + - dx upload ./test_data/fastq/xsmall/Q-Y5F6_1M.R{1,2}.fastq.gz --path /ci-env/input/ --parents --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} - > dx run nf-dxapp-bicf --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} \ --watch \ --delay-workspace-destruction \ --instance-type mem1_ssd1_v2_x16 \ - --input-json "$(envsubst < ./docs/nxf_dnanexus-ci-test.json)" - - curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-active-success?style=flat > ./badges/env/dnanexus.svg + --input-json "$(envsubst < ./docs/nxf_dnanexus-ci-test.json)" \ + > dx.log + - jobID=$(cat dx.log | grep -oP "Job ID: \K.*") + - dx watch ${jobID} + - status=$(dx find executions --id ${jobID} --state failed --brief) + - > + if [ ${status} == "" ] + then + curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-success-success?style=flat > ./badges/env/dnanexus.svg + else + curl --request GET https://img.shields.io/badge/Envronment%3A%20DNAnexus-failed-critical?style=flat > ./badges/env/dnanexus.svg + fi after_script: - module load dxtoolkit/python27/0.294.0 - dx rm /ci-env/auth/c* --all --auth-token ${dnanexus_authToken} --project-context-id ${dnanexus_workspace} diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh index 5d876ed032790d0e3442aed94a0fd79e5e430e60..a730c53de5c1450483f2e4d61f322b64b12674db 100644 --- a/test_data/createTestData.sh +++ b/test_data/createTestData.sh @@ -31,6 +31,14 @@ pigz Q-Y5F6_1M.R2.fastq cp Q-Y5F6_1M.R1.fastq.gz ./NEW_test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz cp Q-Y5F6_1M.R2.fastq.gz ./NEW_test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz +mkdir -p ./NEW_test_data/fastq/xsmall +singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R1.fastq.gz 1000 1> Q-Y5F6_1M.R1.fastq +singularity exec 'docker://gudmaprbk/seqtk1.3:1.0.0' seqtk sample -s100 ./NEW_test_data/fastq/Q-Y5F6.R2.fastq.gz 1000 1> Q-Y5F6_1M.R2.fastq +pigz Q-Y5F6_1M.R1.fastq +pigz Q-Y5F6_1M.R2.fastq +cp Q-Y5F6_1M.R1.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1M.R1.fastq.gz +cp Q-Y5F6_1M.R2.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1M.R2.fastq.gz + mkdir -p ./NEW_test_data/meta singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --illumina --length 35 --basename Q-Y5F6_1M.se -j 20 ./NEW_test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz singularity run 'docker://gudmaprbk/trimgalore0.6.5:1.0.0' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5F6_1M.pe -j 20 ./NEW_test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz ./NEW_test_data/fastq/small/Q-Y5F6_1M.R2.fastq.gz