Switch away from DRMAA to using Snakemake Profiles

[holtgrewe]

Is your feature request related to a problem? Please describe. Using cluster configuration in snakemake is deprecated. Profiles are the future.

Describe the solution you'd like We should switch away from using DRMAA towards using Snakemake Profiles. In particular, the slurm profile is a target.

Describe alternatives you've considered N/A

Additional context N/A

[holtgrewe]

Implementation Plan

• [x] sketch updating the workflows by updating ngs_mapping
• [x] sketch updating the parallel wrappers by updating parallel mutect and dependencies
• [x] sketch updating the overall application
• [x] update documentation

[eudesbarbosa]

Implement unit test for workflows with none

• [x] cbioportal_export
• [x] gene_expression_report
• [x] igv_session_generation
• [x] ngs_data_qc
• [x] panel_of_normals
• [x] somatic_gene_fusion_calling
• [x] somatic_hla_loh_calling
• [x] somatic_purity_ploidy_estimate
• [x] somatic_variant_annotation
• [x] ssomatic_variant_filtration
• [x] somatic_variant_signatures
• [x] somatic_wgs_sv_calling
• [x] targeted_seq_cnv_annotation
• [x] targeted_seq_cnv_export
• [x] variant_checking
• [x] variant_combination
• [x] variant_export
• [x] variant_filtration
• [x] wgs_cnv_annotation
• [x] wgs_cnv_export
• [x] wgs_cnv_filtration
• [x] wgs_mei_annotation
• [x] wgs_mei_filtration
• [x] wgs_sv_annotation
• [x] wgs_sv_export
• [x] wgs_sv_filtration

[eudesbarbosa]

Substitute update_cluster() methods

• [x] snappy_pipeline/workflows/cbioportal_export/init.py
• [x] snappy_pipeline/workflows/gene_expression_quantification/init.py
• [x] snappy_pipeline/workflows/hla_typing/init.py
• [x] snappy_pipeline/workflows/ngs_data_qc/init.py
• [x] snappy_pipeline/workflows/panel_of_normals/init.py
• [x] snappy_pipeline/workflows/roh_calling/init.py
• [x] snappy_pipeline/workflows/somatic_gene_fusion_calling/init.py
• [x] snappy_pipeline/workflows/somatic_msi_calling/init.py
• [x] snappy_pipeline/workflows/somatic_purity_ploidy_estimate/init.py
• [x] snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/init.py
• [x] snappy_pipeline/workflows/somatic_variant_annotation/init.py
• [x] snappy_pipeline/workflows/somatic_variant_calling/init.py
• [x] snappy_pipeline/workflows/somatic_variant_filtration/init.py
• [x] snappy_pipeline/workflows/somatic_variant_signatures/init.py
• [x] snappy_pipeline/workflows/somatic_wgs_cnv_calling/init.py
• [x] snappy_pipeline/workflows/somatic_wgs_sv_calling/init.py
• [x] snappy_pipeline/workflows/targeted_seq_cnv_annotation/init.py
• [x] snappy_pipeline/workflows/targeted_seq_cnv_calling/init.py
• [x] snappy_pipeline/workflows/targeted_seq_cnv_export/init.py
• [x] snappy_pipeline/workflows/variant_annotation/init.py
• [x] snappy_pipeline/workflows/variant_calling/init.py
• [x] snappy_pipeline/workflows/variant_checking/init.py
• [x] snappy_pipeline/workflows/variant_combination/init.py
• [x] snappy_pipeline/workflows/variant_denovo_filtration/init.py
• [x] snappy_pipeline/workflows/variant_export/init.py
• [x] snappy_pipeline/workflows/variant_filtration/init.py
• [x] snappy_pipeline/workflows/variant_phasing/init.py
• [x] snappy_pipeline/workflows/wgs_cnv_annotation/init.py
• [x] snappy_pipeline/workflows/wgs_cnv_calling/init.py
• [x] snappy_pipeline/workflows/wgs_cnv_export/init.py
• [x] snappy_pipeline/workflows/wgs_cnv_filtration/init.py
• [x] snappy_pipeline/workflows/wgs_mei_annotation/init.py
• [x] snappy_pipeline/workflows/wgs_mei_calling/init.py
• [x] snappy_pipeline/workflows/wgs_mei_filtration/init.py
• [x] snappy_pipeline/workflows/wgs_sv_annotation/init.py
• [x] snappy_pipeline/workflows/wgs_sv_calling/init.py
• [x] snappy_pipeline/workflows/wgs_sv_export/init.py
• [x] snappy_pipeline/workflows/wgs_sv_filtration/init.py