chore: remove unused workflows (#530)

bihealth · Jul 5, 2024 · fbb3de1 · fbb3de1
1 parent 17c1a87
commit fbb3de1
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Showing 14 changed files with 0 additions and 336 deletions.
diff --git a/docs/index.rst b/docs/index.rst
@@ -68,23 +68,17 @@ Project Info
     step/igv_session_generation
     step/ngs_data_qc
     step/ngs_mapping
-    step/ngs_sanity_checking
     step/somatic_gene_fusion_calling
-    step/somatic_neoepitope_prediction
-    step/somatic_ngs_sanity_checking
     step/somatic_purity_ploidy_estimate
     step/somatic_targeted_seq_cnv_calling
     step/somatic_variant_annotation
     step/somatic_variant_calling
-    step/somatic_variant_checking
-    step/somatic_variant_expression
     step/somatic_variant_filtration
     step/somatic_wgs_cnv_calling
     step/somatic_wgs_sv_calling
     step/sv_calling_targeted
     step/targeted_seq_mei_calling
     step/targeted_seq_repeat_analysis
-    step/tcell_crg_report
     step/variant_annotation
     step/variant_calling
     step/variant_checking

diff --git a/docs/step/ngs_sanity_checking.rst b/docs/step/ngs_sanity_checking.rst
diff --git a/docs/step/somatic_neoepitope_prediction.rst b/docs/step/somatic_neoepitope_prediction.rst
diff --git a/docs/step/somatic_ngs_sanity_checking.rst b/docs/step/somatic_ngs_sanity_checking.rst
diff --git a/docs/step/somatic_variant_checking.rst b/docs/step/somatic_variant_checking.rst
diff --git a/docs/step/somatic_variant_expression.rst b/docs/step/somatic_variant_expression.rst
diff --git a/docs/step/tcell_crg_report.rst b/docs/step/tcell_crg_report.rst
diff --git a/snappy_pipeline/apps/snappy_snake.py b/snappy_pipeline/apps/snappy_snake.py
@@ -29,28 +29,22 @@
     igv_session_generation,
     ngs_data_qc,
     ngs_mapping,
-    ngs_sanity_checking,
     panel_of_normals,
     repeat_expansion,
     somatic_cnv_checking,
     somatic_gene_fusion_calling,
     somatic_hla_loh_calling,
     somatic_msi_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,
     sv_calling_targeted,
     sv_calling_wgs,
-    tcell_crg_report,
     tumor_mutational_burden,
     varfish_export,
     variant_annotation,
@@ -88,26 +82,20 @@
     "ngs_data_qc": ngs_data_qc,
     "panel_of_normals": panel_of_normals,
     "repeat_analysis": repeat_expansion,
-    "ngs_sanity_checking": ngs_sanity_checking,
     "somatic_cnv_checking": somatic_cnv_checking,
     "somatic_gene_fusion_calling": somatic_gene_fusion_calling,
     "somatic_hla_loh_calling": somatic_hla_loh_calling,
     "somatic_msi_calling": somatic_msi_calling,
-    "somatic_neoepitope_prediction": somatic_neoepitope_prediction,
-    "somatic_ngs_sanity_checking": somatic_ngs_sanity_checking,
     "somatic_purity_ploidy_estimate": somatic_purity_ploidy_estimate,
     "somatic_targeted_seq_cnv_calling": somatic_targeted_seq_cnv_calling,
     "somatic_variant_annotation": somatic_variant_annotation,
     "somatic_variant_calling": somatic_variant_calling,
-    "somatic_variant_checking": somatic_variant_checking,
-    "somatic_variant_expression": somatic_variant_expression,
     "somatic_variant_filtration": somatic_variant_filtration,
     "somatic_variant_signatures": somatic_variant_signatures,
     "somatic_wgs_cnv_calling": somatic_wgs_cnv_calling,
     "somatic_wgs_sv_calling": somatic_wgs_sv_calling,
     "sv_calling_targeted": sv_calling_targeted,
     "sv_calling_wgs": sv_calling_wgs,
-    "tcell_crg_report": tcell_crg_report,
     "tumor_mutational_burden": tumor_mutational_burden,
     "varfish_export": varfish_export,
     "variant_annotation": variant_annotation,

diff --git a/snappy_pipeline/workflows/ngs_sanity_checking/__init__.py b/snappy_pipeline/workflows/ngs_sanity_checking/__init__.py
diff --git a/snappy_pipeline/workflows/somatic_neoepitope_prediction/__init__.py b/snappy_pipeline/workflows/somatic_neoepitope_prediction/__init__.py
diff --git a/snappy_pipeline/workflows/somatic_ngs_sanity_checking/__init__.py b/snappy_pipeline/workflows/somatic_ngs_sanity_checking/__init__.py
diff --git a/snappy_pipeline/workflows/somatic_variant_checking/__init__.py b/snappy_pipeline/workflows/somatic_variant_checking/__init__.py
diff --git a/snappy_pipeline/workflows/somatic_variant_expression/__init__.py b/snappy_pipeline/workflows/somatic_variant_expression/__init__.py