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feat!: 237 revive cnvkit #339

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merged 10 commits into from
Jan 23, 2023
Merged

feat!: 237 revive cnvkit #339

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20ecf58
feat!: 237 revive cnvkit #339
ericblanc20 Dec 27, 2022
b9ddd92
Added list of samples, symlink to access file, access, target & antit…
ericblanc20 Dec 29, 2022
8f6b5ff
Discard autobin for hybrid method, add sex & metrics
ericblanc20 Jan 2, 2023
2338243
Fix wrapper logs
ericblanc20 Jan 2, 2023
c301054
After panel_of_normals successful test on Becnel dataset
ericblanc20 Jan 3, 2023
adc2bed
Access separate from cnvkit
ericblanc20 Jan 9, 2023
1511006
Changes to panel of normals
ericblanc20 Jan 11, 2023
405d5e7
Updated CNVkit usage for exome & wgs
ericblanc20 Jan 11, 2023
f7c14f9
Make snakefmt happy
ericblanc20 Jan 11, 2023
cae427d
fix: tbi to vcf_tbi in tests to conform to new convention
ericblanc20 Jan 20, 2023
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7 changes: 7 additions & 0 deletions docs/step/panel_of_normals.rst
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
.. _step_panel_of_normals::

==========================================================
Creation of panel of normals for somatic SNV & CNV calling
==========================================================

.. automodule:: snappy_pipeline.workflows.panel_of_normals
114 changes: 114 additions & 0 deletions snappy_pipeline/workflows/panel_of_normals/Snakefile
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Expand Up @@ -97,3 +97,117 @@ rule panel_of_normals_mutect2_create_panel:
**wf.get_log_file("mutect2", "create_panel"),
wrapper:
wf.wrapper_path("mutect2/create_panel")


# Panel of normals (cnvkit) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# Write out access file (if required, must be run prior to the cnvkit panel of normals)


rule panel_of_normals_access_run:
output:
**wf.get_output_files("access", "run"),
resources:
time=wf.get_resource("access", "run", "time"),
memory=wf.get_resource("access", "run", "memory"),
partition=wf.get_resource("access", "run", "partition"),
log:
**wf.get_log_file("access", "run"),
wrapper:
wf.wrapper_path("cnvkit/access")


# Write out the normals-only results for the normals --------------------------


rule panel_of_normals_cnvkit_target:
input:
unpack(wf.get_input_files("cnvkit", "target")),
output:
**wf.get_output_files("cnvkit", "target"),
threads: wf.get_resource("cnvkit", "target", "threads")
resources:
time=wf.get_resource("cnvkit", "target", "time"),
memory=wf.get_resource("cnvkit", "target", "memory"),
partition=wf.get_resource("cnvkit", "target", "partition"),
log:
**wf.get_log_file("cnvkit", "target"),
params:
args=wf.substep_dispatch("cnvkit", "get_args", "target"),
wrapper:
wf.wrapper_path("cnvkit/target")


rule panel_of_normals_cnvkit_antitarget:
input:
unpack(wf.get_input_files("cnvkit", "antitarget")),
output:
**wf.get_output_files("cnvkit", "antitarget"),
threads: wf.get_resource("cnvkit", "antitarget", "threads")
resources:
time=wf.get_resource("cnvkit", "antitarget", "time"),
memory=wf.get_resource("cnvkit", "antitarget", "memory"),
partition=wf.get_resource("cnvkit", "antitarget", "partition"),
log:
**wf.get_log_file("cnvkit", "antitarget"),
params:
args=wf.substep_dispatch("cnvkit", "get_args", "antitarget"),
wrapper:
wf.wrapper_path("cnvkit/antitarget")


rule panel_of_normals_cnvkit_coverage:
input:
unpack(wf.get_input_files("cnvkit", "coverage")),
output:
**wf.get_output_files("cnvkit", "coverage"),
threads: wf.get_resource("cnvkit", "coverage", "threads")
resources:
time=wf.get_resource("cnvkit", "coverage", "time"),
memory=wf.get_resource("cnvkit", "coverage", "memory"),
partition=wf.get_resource("cnvkit", "coverage", "partition"),
log:
**wf.get_log_file("cnvkit", "coverage"),
params:
args=wf.substep_dispatch("cnvkit", "get_args", "coverage"),
wrapper:
wf.wrapper_path("cnvkit/coverage")


# Create the panel of normals -------------------------------------------------


rule panel_of_normals_cnvkit_create_panel:
input:
unpack(wf.get_input_files("cnvkit", "create_panel")),
output:
**wf.get_output_files("cnvkit", "create_panel"),
threads: wf.get_resource("cnvkit", "create_panel", "threads")
resources:
time=wf.get_resource("cnvkit", "create_panel", "time"),
memory=wf.get_resource("cnvkit", "create_panel", "memory"),
partition=wf.get_resource("cnvkit", "create_panel", "partition"),
log:
**wf.get_log_file("cnvkit", "create_panel"),
params:
args=wf.substep_dispatch("cnvkit", "get_args", "create_panel"),
wrapper:
wf.wrapper_path("cnvkit/reference")


rule panel_of_normals_cnvkit_report:
input:
unpack(wf.get_input_files("cnvkit", "report")),
output:
**wf.get_output_files("cnvkit", "report"),
threads: wf.get_resource("cnvkit", "report", "threads")
resources:
time=wf.get_resource("cnvkit", "report", "time"),
memory=wf.get_resource("cnvkit", "report", "memory"),
partition=wf.get_resource("cnvkit", "report", "partition"),
log:
**wf.get_log_file("cnvkit", "report"),
params:
args=wf.substep_dispatch("cnvkit", "get_args", "report"),
wrapper:
wf.wrapper_path("cnvkit/report")
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