Implements .command.* save in results/

[cgpu]

Description

Current updates almost all tool version used in the pipelines and moves all docker containers to dockerhub/anczukowlab repository.

Addresses issues:

1. Important

• [x] #242 Implements dedicated folder for .command.*{err,sh,log} Nextflow execution files
• [x] #256 Fixes .bw file duplication

2. Enhancments

• [x] #257 Adds a step in the CI to print the tree view of the results folder that helps spot unexpected file structure or naming
• [x] #258 Sets failure strategy in CI to fail-fast: false

Testing

Pipeline is successfully tested locally with docker and singularity options:

NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,docker

NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,singularity

To test

Pipeline still has to be tested on sumner. Also options to run pipeline with pulling data from SRA and other sources should be tested.

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git checkout save-.command.-logs
nextflow run . -profile  ultra_quick_test,sumner

The command above should be run using the latest version of anczukowlab/splicing-pipelines-nf container

[Vlad-Dembrovskyi]

Why does the PR description say this? Couldn't see any tools updated or containers changed. Looks like a remnant of copy-paste from another PR

Current updates almost all tool version used in the pipelines and moves all docker containers to dockerhub/anczukowlab repository.