Updates all tools and moves docker containers to anczukowlab repo

[Vlad-Dembrovskyi]

Description

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

Solves issues:

• resolves #233
• resolves #234
• resolves #235
• resolves #249
• resolves #236

Updates:

• [x] STAR 2.7.3 -> 2.7.9a
• [x] Samtools 1.10 -> 1.13
• [x] StringTie 2.7.3 -> 2.7.9a
• [x] Gffread 0.11.7 -> 0.12.7
• [x] multiqc 1.8 -> 1.11
• [x] deeptools 3.4.0 -> 3.5.1
• [x] bioconductor-rtracklayer 1.46.0 -> 1.52.0
• [x] gffcompare 0.11.2 -> 0.12.6
• [x] bedtools 2.29.2 -> 2.30.0
• [x] sra-tools 2.10.8 -> 2.11.0
• [x] pigz 2.3.4 -> 2.6.0
• [x] gdc-client 1.5.0 -> 1.6.1

Moves all containers to anczukowlab dockerhub account:

• [x] gcr.io/nextflow-250616/splicing-pipelines-nf -> anczukowlab/splicing-pipelines-nf
• [x] lifebitai/download_reads -> anczukowlab/download_reads
• [x] quay.io/lifebitai/lifebit-ai-fasp -> anczukowlab/lifebit-ai-fasp
• [x] lifebitai/splicing-rmats -> https://hub.docker.com/r/anczukowlab/splicing-rmats

Changes

Since STAR version 2.7.4a STAR requires a new index. So all previously used STAR indices will have to be rebuilt with new version of STAR to work correctly.

The start index used for the ultra_quick_test is already rebuilt and set in profile with this PR. All other indices will have to be updated additionally.

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 vlad-updates-tools
nextflow run . -profile  ultra_quick_test,sumner

Other tests should be performed only after updating the STAR indices they are using. Command to create new star index:

STAR   --runMode genomeGenerate   --runThreadN 2   --genomeDir star/   --genomeFastaFiles genome.fa --sjdbGTFfile genes.gtf

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

[angarb]

Successful run on Sumner with real dataset: N E X T F L O W ~ version 21.04.3 Launching /projects/anczukow-lab/angarb/splicing-pipelines-nf/main.nf [scruffy_plateau] - revision: a8627051fa

[Vlad-Dembrovskyi]

New images successfully pulled by singularity on sumner