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

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Dec 23, 2022
Merged

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

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12 changes: 12 additions & 0 deletions snappy_pipeline/workflows/targeted_seq_cnv_calling/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand 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 ------------------------------------------------------------------------


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12 changes: 6 additions & 6 deletions snappy_pipeline/workflows/variant_annotation/__init__.py
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Expand Up @@ -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
[...]

====================
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171 changes: 0 additions & 171 deletions snappy_pipeline/workflows/variant_calling/Snakefile
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Expand Up @@ -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) --------------------


Expand Down Expand Up @@ -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 ----------------------------------------------
Expand Down
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