Pipeline release v2.0

[Vlad-Dembrovskyi]

v 2.0 - Pipeline improvements

Improvements:

• Adds saving of all the process .command* log files to results/process-logs folder (#251)
• Adds pipeline workdir --cleanup option to clear all intermediate files on pipeline successful completion (true by default, false for CloudOS) (#238, #284, 089d6e3)
• Adds pipeline --error_strategy parameter to be able to specify pipeline error strategy directly from command line (doesn't work if specified in config linked by -c or -config nextflow params) (#267)
• Parametrizes google executor parameters so that pipeline can now be run on different CloudOS environments (#281)
• Adds a new --download_from option FTP mode to download SRA samples from EBI FTP (#283)
  • Adds new parameter -save_unmapped that makes saving of STAR unmapped files optional (false by default) (#284)

Fixes:

• Adds missing trimmomatic logs to the multiqc report (#244)
• Implemented correct support for input strandness in star process when --stranded is second-strand (was hardcoded to strType=2 and only supported first-strand or false before) (#264)
• Issue that stringti_merged results folder as well as some other folders are missing all or some files (#263)
• Fix pipeline crash when params.stranded was set to false (#276)
• Fixes old parameters in google.config that were undesirably overwriting nextflow.config parameters on CloudOS (#281, 217e202)

Updates:

• Updates the following tools: (#248)
  • STAR 2.7.3 -> 2.7.9a NOTE: Requires a new index! (updated in test profile)
  • Samtools 1.10 -> 1.13
  • StringTie 2.1.3b -> 2.1.7
  • Gffread 0.11.7 -> 0.12.7
  • multiqc 1.8 -> 1.11
  • deeptools 3.4.0 -> 3.5.1
  • bioconductor-rtracklayer 1.46.0 -> 1.52.0
  • gffcompare 0.11.2 -> 0.12.6
  • bedtools 2.29.2 -> 2.30.0
  • sra-tools 2.10.8 -> 2.11.0
  • pigz 2.3.4 -> 2.6.0
  • gdc-client 1.5.0 -> 1.6.1
• Moves all containers to https://hub.docker.com/u/anczukowlab

Maintenance:

• Consideably reduces number of basic redundant CI tests by removing completely the max_retries matrix and push from on: [push, pull_request]
• Adds CI test for sra-downloading pipeline pathway (only supported with docker profile for now) (#253)

To test

Pull the repository

git clone https://github.com/TheJacksonLaboratory/splicing-pipelines-nf
cd splicing-pipelines-nf
git checkout dev

Run the test profile with docker

NXF_VER=20.01.0 nextflow run . -profile ultra_quick_test,docker

Tested on sumner (JAX HPC) and approved by @angarb here: link

[Vlad-Dembrovskyi]

First successful big run in non-ctrl env: https://cloudos.lifebit.ai/app/jobs/61710bd31b866a01d6a27216 (public link: https://cloudos.lifebit.ai/public/jobs/61710bd31b866a01d6a27216)

[Vlad-Dembrovskyi]

Successful runs by @angarb of tests in ctrl env: https://cloudos.lifebit.ai/public/jobs/617175711b866a01d6a320b1 https://cloudos.lifebit.ai/public/jobs/617177d31b866a01d6a328bd

[Vlad-Dembrovskyi]

Latest test from Britanny on CloudOS shows we are good to go for now. GTEX issues and improvements will be addressed in next release.

https://cloudos.lifebit.ai/public/jobs/619bbaa4fb26cf01dcee8446