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Tumour only mode for variant calling#43

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RaqManzano wants to merge 26 commits intodevfrom
tumour_only
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Tumour only mode for variant calling#43
RaqManzano wants to merge 26 commits intodevfrom
tumour_only

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@RaqManzano RaqManzano commented Oct 22, 2024

Here I have implemented a tumour-only mode that I have successfully used for some cases. However, to merge to dev there is still work to do:

  • This branch is not in sync with dev, some conflicts when merging are expected.
  • Testing is needed, there is something is place but it is simple.
  • Review of workflow is needed to make sure nothing is broken when in paired mode.

Help is very welcome as I won't be able to continue with this for a few months.

This pull request is to solve #37

@RaqManzano RaqManzano added enhancement New feature or request help wanted Extra attention is needed labels Oct 22, 2024
@RaqManzano RaqManzano self-assigned this Oct 22, 2024
@RaqManzano RaqManzano linked an issue Oct 22, 2024 that may be closed by this pull request
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@RaqManzano RaqManzano mentioned this pull request Oct 22, 2024
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RaqManzano commented Nov 4, 2024

Things to check:

  • This line might give error when using S3 in prepare_genome subworkflow

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 2.14.1.
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.

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Add tumour-only mode

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