Support PRIDE / SDRF input

[jonasscheid]

PR to fix #277

Key implementations:

• Provide PRIDE id only (if SDRF is present in PRIDE archive) or provide SDRF containg paths to the pride archive.
• Automatically fetch data via pridepy
• Convert SDRF to mhcquant samplesheet + new search preset tsv via sdrf-pipelines export function
• Seamlessly plug data and metadata into the exiting channels

Steps happen during the PIPELINE_INITIALISATION subworkflow.
Tested successfully on PXD009752 (2 raw files), and PXD004894 (140 raw files)

Edit: WIP figuring out which Comet resource limits fit best for CI runners for the sdrf test
Edit edit: New test runs through, but no space on device. Will shrink sdrf sheet to only 1 file instead of 2 after review

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[ypriverol]

@have you tested pridepy with aspera in production? How does it works?

[jonasscheid]

@ypriverol I did (on my VM (IPv6)) for 140 raw files:

Protocol	Wall time (140 files, 5-way parallel)	Avg per file	Effective throughput
FTP	58 min (3498 s)	122 s	~50 MB/s aggregate
Aspera	146 min (8778 s)	308 s	~20 MB/s aggregate

[d4straub]

Looks good.
Nothing serious, but I dislike the resource allocations in conf/modules.conf.
And the usage.md might benefit from input documentation.
About Edit edit: New test runs through, but no space on device. Will shrink sdrf sheet to only 1 file instead of 2 after review: Afaik its possible to increase the size of the runner disk so that this wont happen (dont remember details, somewhere in the nf-core slack I think) but if you can adjust test files, thats preferable ofc.

I approve and think you will do whats necessary, if anything.

[jonasscheid]

Thanks @d4straub !

faik its possible to increase the size of the runner disk so that this wont happen (dont remember details, somewhere in the nf-core slack I think) but if you can adjust test files, thats preferable ofc.

I think thats when nf-core comes into p(l)ay :D. Not sure if that would be needed in this setting. I'll try to reduce the test input further: Could we try this? nf-core/test-datasets#2007