Fix xsmall fastqs

.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 \

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