CIBERER / GdTBioinfo-nf-snvs

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[FEATURE] Add a subworkflow for Variant Calling steps #5

Closed yolandabq closed 2 months ago

yolandabq commented 7 months ago

Which type of feature are you implementing?

[X] I have selected (at least) one of the following Label for the feature

Is there an existing issue / PR for this?

[X] I have searched for existing issues
[X] I have searched for existing PRs

Is there already an implementation for this feature?

[x] I have searched for existing nf-modules
[X] I have searched for existing biocontainers

Describe the feature

Subworkflow that runs all the steps of variant calling:

Run Gatk Haplotypecaller, DeepVariant and Gatk Haplotypecaller Dragen
Process of vcfs: SelectVariants, VariantFiltration, SortVcf
Merge Vcfs

Background

No response

Proposed implementation

Adaptar el workflow SNV_CALLING (línea 408): https://github.com/TBLabFJD/NextVariantFJD/blob/main/main.nf Sacarlo del main.nf y hacer un subworkflow en la carpeta correspondiente del template de nf-core.

Anything else?

No response

Related Issues

1 #2 #3 #4 #6 #7 #8

Are you going to work on this?

[ ] If I'm planning to work on this feature, I added myself to the Assignees to facilitate tracking who is working on this.

yolandabq commented 2 months ago

En vez de un subworkflow con todos los variant caller, vamos a hacer un subworkflow por variant caller y los iremos ejecutando según elija el usuario (uno, dos o los 3).