Remove commented-out/obsolete CnvKit code

hammerlab · Aug 21, 2017 · b234f5b · b234f5b
1 parent 73d52a7
commit b234f5b
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Showing 5 changed files with 0 additions and 180 deletions.
diff --git a/src/bfx_tools/cnvkit.ml b/src/bfx_tools/cnvkit.ml
diff --git a/src/environment_setup/bioconda.ml b/src/environment_setup/bioconda.ml
@@ -48,6 +48,4 @@ let default ~host ~run_program ~install_path () =
       ~check_bin:"seq2HLA" Default.seq2hla;
     create_bioconda_tool ~host ~run_program ~install_path
       ~check_bin:"snpEff" Default.snpeff;
-    create_bioconda_tool ~host ~run_program ~install_path
-      ~check_bin:"cnvkit.py" Default.cnvkit;
   ])
diff --git a/src/pipeline_edsl/semantics.ml b/src/pipeline_edsl/semantics.ml
@@ -331,15 +331,6 @@ module type Bioinformatics_base = sig
   val seqtk_shift_phred_scores:
     [ `Fastq ] repr ->
     [ `Fastq ] repr
-(*
-  val cnvkit:
-    ?region_size: int ->
-    normal: [ `Bam ] repr ->
-    tumor: [ `Bam ] repr ->
-    reference_build: string ->
-    unit ->
-    [ `Cnv_kit ] repr
-  *)
 
 end
 
diff --git a/src/pipeline_edsl/to_workflow.ml b/src/pipeline_edsl/to_workflow.ml
@@ -30,8 +30,6 @@ module File_type_specification = struct
     | Bai: single_file workflow_node -> t
     | Kallisto_result: single_file workflow_node -> t
     | Cufflinks_result: single_file workflow_node -> t
-    | Cnvkit_result:
-        Biokepi_bfx_tools.Optitype.product workflow_node -> t
     | Raw_file: single_file workflow_node -> t
     | Gz: t -> t
     | List: t list -> t
@@ -61,7 +59,6 @@ module File_type_specification = struct
     | Bai _ -> "Bai"
     | Kallisto_result _ -> "Kallisto_result"
     | Cufflinks_result _ -> "Cufflinks_result"
-    | Cnvkit_result _ -> "Cnvkit_result"
     | Raw_file _ -> "Input_url"
     | Gz a -> sprintf "(gz %s)" (to_string a)
     | List l ->
@@ -203,7 +200,6 @@ module File_type_specification = struct
     | Cufflinks_result wf -> one_depends_on wf
     | Bai wf -> one_depends_on wf
     | Kallisto_result wf -> one_depends_on wf
-    | Cnvkit_result wf -> one_depends_on wf
     | MHC_alleles wf -> one_depends_on wf
     | Raw_file w -> one_depends_on w
     | List l -> List.concat_map l ~f:as_dependency_edges
@@ -1190,31 +1186,6 @@ module Make (Config : Compiler_configuration)
     )
     |> AF.with_provenance "seqtk-shift-phred-scores"
       ["fastq", AF.get_provenance fastq]
-(*
-  let cnvkit 
-      ?(region_size=Tools.Cnvkit.default_region_size)
-      ~normal_bams ~tumor_bams ~reference_build
-    =
-    let nbams = List.map ~f:get_bam normal_bams in
-    let tbams = List.map ~f:get_bam tumor_bams in
-    let run_name = 
-      let l = List.length in
-      sprintf "%d-normal-%d-tumor" (l nbams) (l tbams)
-    in
-    let output_folder =
-      Name_file.in_directory Config.work_dir
-        ~readable_suffix:"cnvkit" 
-          [ run_name; reference_build; string_of_int region_size ]
-    in
-    Cnvkit_result (
-      Tools.Cnvkit.batch
-        ~normal_bams
-        ~tumor_bams
-        ~reference_build
-        ~run_name
-        ~output_folder
-    )
-  *)
 
   let seq2hla fq =
     let fastq = get_fastq (AF.get_file fq) in

diff --git a/src/run_environment/machine.ml b/src/run_environment/machine.ml
@@ -66,7 +66,6 @@ module Tool = struct
     let seq2hla = create "seq2hla" ~version:"2.2"
     let picard = create "picard" ~version:"2.9.2"
     let snpeff = create "snpeff" ~version:"4.3.1m-0"
-    let cnvkit = create "cnvkit" ~version:"0.8.6a0"
     (* PyPI packages *)
     let pyensembl = create "pyensembl" ~version:"1.1.0"
     let vcfannotatepolyphen = create "vcf-annotate-polyphen" ~version:"0.1.2"