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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: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Revert "add pipeline nf-test"
…ng issues Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
…y and
${meta_id}_jointcall
bam-sv_variant_calling
results/
└── sawfish/
├── sample1/
│ ├── sample1_discovery/
│ └── sample1_jointcall/
└── sample2/
├── sample2_discovery/
└── sample2_jointcall/
Add variant calls and methylation features, update modules, compliance with `nf-core/tools` template 3.5.1
Update README.md
…nfig to pacvar's test-dataset base path
Enhance testing: add test_wgs_hificnv.config to test HiFiCNV and sawfish's cnv calling
add the corresponding PR # section titles that are for for 1.1.0dev.
Rename pipeline parameter `skip_cnv` to `skip_hificnv`
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Do not merge! This is a PR of dev compared to the TEMPLATE branch for whole-pipeline reviewing purposes. Changes should be made to dev and this PR should not be merged into first-commit-for-pseudo-pr!