Env.ci

Make environment tests for DNAnexus and AWS

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipeline integrated_pe artifact
• [ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
• [ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
• CHANGELOG.md is updated
• README.md is updated
• [ ] LICENSE.md is updated with new contributors
• [ ] Docker images moved to production release and changed in pipeline
• [ ] Docker images used in the CI unit tests match those used in pipeline

• ~~[ ] Close issue~~ Closes #

/cc @ghenry @venkat.malladi

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