diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 587a25ed9cb63df11da78d05089ffe01881e9c89..b63a579db18544ff7625bfd22adae3f218460703 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -49,8 +49,8 @@ getData: script: - 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.zip - - singularity run 'docker://gudmaprbk/deriva1.3:1.0.0' bash ./workflow/scripts/bdbagFetch.sh Q-Y5F6 Q-Y5F6 TEST + - 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 - pytest -m getData artifacts: name: "$CI_JOB_NAME" @@ -655,7 +655,7 @@ override_inputBag: script: - hostname - ulimit -a - - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Replicate_Q-Y5F6.zip --upload false --ci true + - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --inputBagForce ./test_data/bag/staging/Q-Y5F6_inputBag_20201228.zip --upload false --ci true - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_PE_multiqc_data.json \; artifacts: name: "$CI_JOB_NAME" diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index b09ee5f6208345d7895f290222fe999281a380e9..30f9bd126b7ec602381de244a1eab301845e8e84 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -231,7 +231,7 @@ process getData { echo -e "LOG: linked" >> ${repRID}.getData.log # get bag basename - replicate=\$(basename "${inputBag}" | cut -d "_" -f1) + replicate=\$(basename "${inputBag}") echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log # unzip bag diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh index 2a0ee96f58b392a2b8de0e37c31f8a2a42f4e359..606b88397d5a6cf4feb4aa38d7615e3e3ba48735 100644 --- a/workflow/scripts/bdbagFetch.sh +++ b/workflow/scripts/bdbagFetch.sh @@ -2,7 +2,7 @@ if [ -z "${3}" ] then - bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag + bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1} for i in $(find */ -name "*R*.fastq.gz") do path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz") @@ -10,5 +10,5 @@ then done elif [ "${3}" == "TEST" ] then - bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}_inputBag + bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1} fi