`cubi-tk snappy`is not yet adapted to new/renamed snappy steps

[Nicolai-vKuegelgen]

Describe the bug The snappy step dependencies in cubi-tk/snappy/common do currently not fully match the state of snappy. This means that i.e. cubi-tk snappy kickoffwill not start certain steps, other tools may be affected as well.

These currently defined steps have been renamed in or removed from snappy:

• roh_calling [removed without replacement?]
• variant_export
• targeted_seq_cnv_calling
• targeted_seq_cnv_annotation
• targeted_seq_cnv_export
• wgs_sv_calling
• wgs_sv_annotation
• wgs_sv_export
• wgs_cnv_calling
• wgs_cnv_annotation
• wgs_cnv_export

These steps in snappy are likely replacements or additions that may need definition in cubi-tk

• helper_gcnv_model_targeted & helper_gcnv_model_wgs
  • newly added steps (?)
• sv_calling_targeted
  • replaces: targeted_seq_cnv_calling
• sv_calling_wgs
  • replaces: wgs_sv_calling & wgs_cnv_calling
• varfish_export
  • replaces: wgs_sv_export & wgs_cnv_export & (?) targeted_seq_cnv_export
• variant_annotation
  • replaces: wgs_sv_annotation, wgs_cnv_annotation & (?) targeted_seq_cnv_annotation
• variant_export_external
  • likely a replacement for wgs_cnv_export_external & wgs_sv_export_external, though those are still in use?
• variant_checking, variant_denovo_filtration, variant_filtration, variant_phasing
  • unclear if cubi-tk support is needed?

Support for these steps was not included in cubi-tk and is probably not needed:

• General NGS: adapter_trimming, ngs_data_qc, ngs_mapping, ngs_sanity_checking,
• RNAseq: gene_expression_quantification, gene_expression_report
• Various: cbioportal_export, hla_typing, tcell_crg_report, igv_session_generation, panel_of_normals, repeat_analysis
• somatic_*:
  • somatic_hla_loh_calling, somatic_msi_calling, somatic_gene_fusion_calling, somatic_neoepitope_prediction, somatic_ngs_sanity_checking, somatic_purity_ploidy_estimate, somatic_targeted_seq_cnv_calling, somatic_variant_annotation, somatic_variant_calling, somatic_variant_checking, somatic_variant_expression, somatic_variant_filtration, somatic_variant_signatures, somatic_wgs_cnv_calling, somatic_wgs_sv_calling,

To Reproduce Steps to reproduce the behavior:

1. Create a snappy project with of the currently not supported steps
2. run cubi-tk snappy kickoff The unsupported steps will not be run.

Expected behavior Cubi-tk should be updated to have support for at least all steps used in routine analysis of WGS & WES data for genetics. A likely list of steps that should ahve support is given above.

[xiamaz]

Yes, am currently experiencing similar issues with a legacy pipeline with steps named helper_gcnv_model_targeted, sv_calling_targeted and varfish_export