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

bihealth · Dec 30, 2022 · f87c8bb · f87c8bb
1 parent 99dae5f
commit f87c8bb
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Showing 11 changed files with 197 additions and 589 deletions.
diff --git a/docs/index.rst b/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

diff --git a/docs/step/roh_calling.rst b/docs/step/roh_calling.rst
diff --git a/snappy_pipeline/apps/snappy_snake.py b/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,

diff --git a/snappy_pipeline/workflows/roh_calling/Snakefile b/snappy_pipeline/workflows/roh_calling/Snakefile
diff --git a/snappy_pipeline/workflows/roh_calling/__init__.py b/snappy_pipeline/workflows/roh_calling/__init__.py