feat: remove legacy variant callers (#295) (#297)

bihealth · Dec 23, 2022 · fa2fc6c · fa2fc6c
1 parent 6f2edd7
commit fa2fc6c
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Showing 40 changed files with 26 additions and 2,352 deletions.
diff --git a/snappy_pipeline/workflows/targeted_seq_cnv_calling/Snakefile b/snappy_pipeline/workflows/targeted_seq_cnv_calling/Snakefile
@@ -28,6 +28,8 @@ wf = TargetedSeqCnvCallingWorkflow(workflow, config, lookup_paths, config_paths,
 localrules:
     # Linking files from work/ to output/ should be done locally
     targeteq_seq_cnv_calling_link_out_run,
+    # Writing out pedigrees can be done locally
+    wgs_cnv_calling_write_pedigree_run,
 
 
 rule all:
@@ -51,6 +53,16 @@ rule targeteq_seq_cnv_calling_link_out_run:
 
 # Germline CNV Calling ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+# Write out pedigree file -----------------------------------------------------
+
+
+rule wgs_cnv_calling_write_pedigree_run:
+    output:
+        wf.get_output_files("write_pedigree", "run"),
+    run:
+        wf.substep_dispatch("write_pedigree", "run", wildcards, output)
+
+
 # XHMM ------------------------------------------------------------------------
 
 

diff --git a/snappy_pipeline/workflows/variant_annotation/__init__.py b/snappy_pipeline/workflows/variant_annotation/__init__.py
@@ -35,17 +35,17 @@
 - ``{mapper}.{var_caller}.{var_annotator}.{lib_name}.vcf.gz.tbi.md5``
 
 
-For example, annotation of freebayes variant calls could look like this:
+For example, annotation of gatk_hc variant calls could look like this:
 
 ::
 
     output/
-    +-- bwa.freebayes.jannovar_annotate_vcf.P001-N1-DNA1-WES1
+    +-- bwa.gatk_hc.jannovar_annotate_vcf.P001-N1-DNA1-WES1
     |   `-- out
-    |       |-- bwa.freebayes.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz
-    |       |-- bwa.freebayes.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.tbi
-    |       |-- bwa.freebayes.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.md5
-    |       `-- bwa.freebayes.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.tbi.md5
+    |       |-- bwa.gatk_hc.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz
+    |       |-- bwa.gatk_hc.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.tbi
+    |       |-- bwa.gatk_hc.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.md5
+    |       `-- bwa.gatk_hc.jannovar_annotate_vcf.P001-N1-DNA1-WES1.vcf.gz.tbi.md5
     [...]
 
 ====================

diff --git a/snappy_pipeline/workflows/variant_calling/Snakefile b/snappy_pipeline/workflows/variant_calling/Snakefile
@@ -84,27 +84,6 @@ rule variant_calling_bcftools_run:
         wf.wrapper_path("bcftools_call")
 
 
-# Run FreeBayes ---------------------------------------------------------------
-
-
-rule variant_calling_freebayes_run:
-    input:
-        unpack(wf.get_input_files("freebayes", "run")),
-    output:
-        **wf.get_output_files("freebayes", "run"),
-    threads: wf.get_resource("freebayes", "run", "threads")
-    resources:
-        time=wf.get_resource("freebayes", "run", "time"),
-        memory=wf.get_resource("freebayes", "run", "memory"),
-        partition=wf.get_resource("freebayes", "run", "partition"),
-    params:
-        **wf.get_params("freebayes", "run")(),
-    log:
-        **wf.get_log_file("freebayes", "run"),
-    wrapper:
-        wf.wrapper_path("freebayes")
-
-
 # Run GATK HaplotypeCaller (direct, pedigree/multi-sample) --------------------
 
 
@@ -149,156 +128,6 @@ rule variant_calling_gatk_ug_run:
         wf.wrapper_path("gatk_ug_par")
 
 
-# Run Platypus ---------------------------------------------------------------
-
-
-rule variant_calling_platypus_run:
-    input:
-        unpack(wf.get_input_files("platypus", "run")),
-    output:
-        **wf.get_output_files("platypus", "run"),
-    threads: wf.get_resource("platypus", "run", "threads")
-    resources:
-        time=wf.get_resource("platypus", "run", "time"),
-        memory=wf.get_resource("platypus", "run", "memory"),
-        partition=wf.get_resource("platypus", "run", "partition"),
-    log:
-        **wf.get_log_file("platypus", "run"),
-    wrapper:
-        wf.wrapper_path("platypus/germline")
-
-
-# Run GATK HaplotypeCaller GVCF Generation ------------------------------------
-
-
-rule variant_calling_gatk_hc_gvcf_discovery:
-    input:
-        unpack(wf.get_input_files("gatk_hc_gvcf", "discover")),
-    output:
-        **wf.get_output_files("gatk_hc_gvcf", "discover"),
-    threads: wf.get_resource("gatk_hc_gvcf", "discover", "threads")
-    resources:
-        time=wf.get_resource("gatk_hc_gvcf", "discover", "time"),
-        memory=wf.get_resource("gatk_hc_gvcf", "discover", "memory"),
-        partition=wf.get_resource("gatk_hc_gvcf", "discover", "partition"),
-    params:
-        step_key="variant_calling",
-        caller_key="gatk_hc_gvcf",
-    log:
-        wf.get_log_file("gatk_hc_gvcf", "discover"),
-    wrapper:
-        wf.wrapper_path("gatk_hc_gvcf_par/discovery")
-
-
-# Run GATK HaplotypeCaller GVCF Pedigree Genotyping ---------------------------
-
-
-rule variant_calling_gatk_hc_gvcf_genotype_pedigree:
-    input:
-        unpack(wf.get_input_files("gatk_hc_gvcf", "genotype_pedigree")),
-    output:
-        **wf.get_output_files("gatk_hc_gvcf", "genotype_pedigree"),
-    threads: wf.get_resource("gatk_hc_gvcf", "genotype_pedigree", "threads")
-    resources:
-        time=wf.get_resource("gatk_hc_gvcf", "genotype_pedigree", "time"),
-        memory=wf.get_resource("gatk_hc_gvcf", "genotype_pedigree", "memory"),
-        partition=wf.get_resource("gatk_hc_gvcf", "genotype_pedigree", "partition"),
-    params:
-        step_key="variant_calling",
-        caller_key="gatk_hc_gvcf",
-    log:
-        wf.get_log_file("gatk_hc_gvcf", "genotype_pedigree"),
-    wrapper:
-        wf.wrapper_path("gatk_hc_gvcf_par/genotyping")
-
-
-# Run GATK HaplotypeCaller Cohort CombineGVCFs --------------------------------
-
-# Collect cohort-wide GVCF file to circumvent problems with file handle counts
-# downstream.
-
-
-rule variant_calling_gatk_hc_gvcf_combine_gvcf:
-    input:
-        unpack(wf.get_input_files("gatk_hc_gvcf", "combine_gvcf")),
-    output:
-        **wf.get_output_files("gatk_hc_gvcf", "combine_gvcf"),
-    threads: wf.get_resource("gatk_hc_gvcf", "combine_gvcf", "threads")
-    resources:
-        time=wf.get_resource("gatk_hc_gvcf", "combine_gvcf", "time"),
-        memory=wf.get_resource("gatk_hc_gvcf", "combine_gvcf", "memory"),
-        partition=wf.get_resource("gatk_hc_gvcf", "combine_gvcf", "partition"),
-    params:
-        args=wf.substep_dispatch("gatk_hc_gvcf", "get_args", "combine_gvcf"),
-    log:
-        wf.get_log_file("gatk_hc_gvcf", "combine_gvcf"),
-    wrapper:
-        wf.wrapper_path("gatk_hc_gvcf_par/combine_gvcf")
-
-
-# Run GATK HaplotypeCaller GVCF Cohort Genotyping -----------------------------
-
-
-rule variant_calling_gatk_hc_gvcf_genotype_cohort:
-    input:
-        wf.get_input_files("gatk_hc_gvcf", "genotype_cohort"),
-    output:
-        **wf.get_output_files("gatk_hc_gvcf", "genotype_cohort"),
-    threads: wf.get_resource("gatk_hc_gvcf", "genotype_cohort", "threads")
-    resources:
-        time=wf.get_resource("gatk_hc_gvcf", "genotype_cohort", "time"),
-        memory=wf.get_resource("gatk_hc_gvcf", "genotype_cohort", "memory"),
-        partition=wf.get_resource("gatk_hc_gvcf", "genotype_cohort", "partition"),
-    log:
-        wf.get_log_file("gatk_hc_gvcf", "genotype_cohort"),
-    wrapper:
-        wf.wrapper_path("gatk_hc_gvcf_par/genotyping")
-
-
-# Run Varscan Pedigree-Wise ---------------------------------------------------
-
-
-rule variant_calling_varscan_call_pedigree:
-    input:
-        unpack(wf.get_input_files("varscan", "call_pedigree")),
-    output:
-        **wf.get_output_files("varscan", "call_pedigree"),
-    threads: wf.get_resource("varscan", "call_pedigree", "threads")
-    resources:
-        time=wf.get_resource("varscan", "call_pedigree", "time"),
-        memory=wf.get_resource("varscan", "call_pedigree", "memory"),
-        partition=wf.get_resource("varscan", "call_pedigree", "partition"),
-    params:
-        step_key="variant_calling",
-        caller_key="varscan",
-    log:
-        **wf.get_log_file("varscan", "call_pedigree"),
-    wrapper:
-        wf.wrapper_path("varscan_par/call_joint")
-
-
-# Run Varscan Cohort-Wide -----------------------------------------------------
-
-
-rule variant_calling_varscan_call_cohort:
-    input:
-        wf.get_input_files("varscan", "call_cohort"),
-    output:
-        **wf.get_output_files("varscan", "call_cohort"),
-    threads: wf.get_resource("varscan", "call_cohort", "threads")
-    resources:
-        time=wf.get_resource("varscan", "call_cohort", "time"),
-        memory=wf.get_resource("varscan", "call_cohort", "memory"),
-        partition=wf.get_resource("varscan", "call_cohort", "partition"),
-    params:
-        step_key="variant_calling",
-        caller_key="varscan",
-    log:
-        **wf.get_log_file("varscan", "call_cohort"),
-    wrapper:
-        wf.wrapper_path("varscan_par/call_joint")
-
-
 # QC / Statistics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 # Generate BCFtools stats report ----------------------------------------------