Move to nf-core sbwf GLIMPSE1

[LouisLeNezet]

PR checklist

Replace #221 and #242
Change to nf-core sbwf for GLIMPSE1
Small change to vcf_index instead of vcf_tbi for consistency.

• 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/phaseimpute 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.

[LouisLeNezet]

Hi @atrigila,
This PR is now ready.
The sbwf vcf_concatenate and bam_gl_bcftools will be moved to nf-core in a futur PR.
The reason the md5sum of the variant changed in test_all for the glimpse imputation is due to the use now of the genetic map.

[atrigila]

The reason the md5sum of the variant changed in test_all for the glimpse imputation is due to the use now of the genetic map.

Where is the usage of the genetic map?

[LouisLeNezet]

I thought we were using the genetic map in the test all config, but not yet...
I will check tomorrow what changed

[LouisLeNezet]

I've found the issue.
The only difference between the two is the presence of --seed 1 argument in GLIMPSE/PHASE.
I've added a commit without the seed for you to see that the diff without did not change anything.

I've put back the seed as we want a better control over this parameter.
This PR should now be ready for review !