diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 03b768f66ff770dccb430bf060cd2daab69dd0f8..32f9e671238d9c55c009c5a18bcd60ff0262ff2c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1028,7 +1028,7 @@ 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/xsmall/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_1K.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} \ --delay-workspace-destruction \ diff --git a/test_data/createTestData.sh b/test_data/createTestData.sh index a730c53de5c1450483f2e4d61f322b64b12674db..60ccf67c8d20d4f3928b42c25cd8bfbb5e4817e3 100644 --- a/test_data/createTestData.sh +++ b/test_data/createTestData.sh @@ -32,12 +32,12 @@ 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 +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_1K.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_1K.R2.fastq +pigz Q-Y5F6_1K.R1.fastq +pigz Q-Y5F6_1K.R2.fastq +cp Q-Y5F6_1K.R1.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1K.R1.fastq.gz +cp Q-Y5F6_1K.R2.fastq.gz ./NEW_test_data/fastq/xsmall/Q-Y5F6_1K.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