refactor!: move "bcftools roh" as report in variant_calling (#310)

README.md

@@ -97,3 +97,9 @@ Moving GenomeAnalysisTK-3.8-1-0-gf15c1c3ef.tar.bz2 to /home/holtgrem_c/miniconda
 ```
 
 You are now ready to run GATK v3 from this environment.
+
+## Development Notes
+
+Here, you can find the required layout for post-PR commit messages:
+
+- https://github.com/amannn/action-semantic-pull-request#configuration

docs/index.rst

@@ -54,7 +54,6 @@ Project Info
     step/ngs_data_qc
     step/ngs_mapping
     step/ngs_sanity_checking
-    step/roh_calling
     step/somatic_gene_fusion_calling
     step/somatic_neoepitope_prediction
     step/somatic_ngs_sanity_checking

snappy_pipeline/apps/snappy_snake.py

@@ -31,7 +31,6 @@
     ngs_sanity_checking,
     panel_of_normals,
     repeat_expansion,
-    roh_calling,
     somatic_gene_fusion_calling,
     somatic_hla_loh_calling,
     somatic_msi_calling,
@@ -100,7 +99,6 @@
     "panel_of_normals": panel_of_normals,
     "repeat_analysis": repeat_expansion,
     "ngs_sanity_checking": ngs_sanity_checking,
-    "roh_calling": roh_calling,
     "somatic_gene_fusion_calling": somatic_gene_fusion_calling,
     "somatic_hla_loh_calling": somatic_hla_loh_calling,
     "somatic_msi_calling": somatic_msi_calling,