TheJacksonLaboratory / splicing-pipelines-nf

Repository for the Anczukow-Lab splicing pipeline

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[DEL 3039] Implement ftp download for SRA accessions (#2) #283

Closed Vlad-Dembrovskyi closed 2 years ago

Vlad-Dembrovskyi commented 2 years ago

Description

A new option was added to the --download_from parameter to include SRA FTP download. The allowed options now include: 'TCGA', 'GTEX' or 'GEN3-DRS', 'SRA', 'FTP'

'FTP 'was used as 'SRA-FTP' was causing collisions with the 'SRA' option

If the 'FTP' option is used, an intermediate process is launched (get_ftp_acccession) where the FTP URL is constructed and the fastq files are downloaded. This interacts with the --singleEnd parameter to adjust for single end or paired end data download.

The sra_test profile was adjusted to this feature could be tested directly. Also - a CI test for singularity with sra_test profile has ben re-enabled.

Documentation was adjusted when relevant to reflect these changes.

Testing

Local

This changes can be tested by running the following commad

nextflow main.nf -profile sra_test,docker

NXF_VER=20.01.0 nextflow run . -profile sra_test,docker

NXF_VER=20.04.1 nextflow run . -profile sra_test,docker

NXF_VER=20.01.0 nextflow run . -profile sra_test,singularity

NXF_VER=20.04.1 nextflow run . -profile sra_test,singularity

CloudOS

https://cloudos.lifebit.ai/app/jobs/6172786e88e0c901db2b2d69

Vlad-Dembrovskyi commented 2 years ago

Th PR is successfully tested by @angarb on sumner and on CloudOS GCP ctrl workspace: [slack thread]

CloudOS: https://cloudos.lifebit.ai/public/jobs/6179a99388e0c901db2f5b3a

Sumner: