Adds sra test

[Vlad-Dembrovskyi]

Description

Adds a new test profile that tests the SRA input download option. Closes #252

Purpose

Pipeline is designed to also support providing input fastq files as SRA accessions and download them with SRA toolkit, but this way of running the pipeline hasn't been covered yet by the CI tests.

Changes

• Adds sra.csv test data and sra_test.config to be run with new profile sra_test
• Removes the docker.runOptions in nextflow.config because sra-toolkit can't be run as non-root user with current container
• Changes the ci tests to run also with sra_test profile (only for docker, as for singularity in ci it always fails)

To test

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git checkout add-sra-test

NXF_VER=20.01.0 nextflow run . -profile base,sra_test,docker

To test on sumner

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git checkout add-sra-test

NXF_VER=20.01.0 nextflow run . -profile base,sra_test,sumner

[Vlad-Dembrovskyi]

I can't undesrstand why both ultra quick test and singularity tests are failing now.

Locally ultra_quick test is running fine: nextflow run . -profile base,ultra_quick_test,docker

[Vlad-Dembrovskyi]

Locally the singularity one is failing too, although with a different error I think it may be due to how sra-toolkit was installed in docker container. sra-toolkit needs some kind of configuration to be run first before using it, and this configuration is user-specific. In the used docker container the sra-toolkit was installed for root user only. So if you are running the container with singularity with not a root user - you don't have the configuration set and that's why it fails. I tried to see how could one set this configuration for new user non-interactively, and I couldn't find a solution so far:

• https://github.com/ncbi/sra-tools/issues/409
• https://github.com/open2c/distiller-nf/issues/157
• https://github.com/ncbi/sra-tools/issues/291

[Vlad-Dembrovskyi]

The remaining SRA tests are finally not failing, @angarb and @cgpu approved the merge for closest release and to leave the singularity<>SRA issue for next release. Merging.