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fix: re-enabling and fixing Popdel
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@holtgrewe
holtgrewe committed Jan 18, 2023
1 parent 47d9e33 commit 2b45596
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Showing 4 changed files with 162 additions and 125 deletions.
10 changes: 7 additions & 3 deletions snappy_pipeline/workflows/common/sv_calling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,10 +50,14 @@ def get_log_file(self, action: typing.Optional[str] = None):
"""Return dict of log files in the "log" directory"""
_ = action
if action and action != self.actions[-1]:
infix = f"{self.name}_{action}"
token = f"{self.name}_{action}"
else:
infix = self.name
prefix = f"work/{{mapper}}.{infix}.{{library_name}}/log/{{mapper}}.{infix}.{{library_name}}.sv_calling"
token = self.name
if hasattr(self, f"_get_log_file_infix_{action}"):
infix = getattr(self, f"_get_log_file_infix_{action}")()
else:
infix = f"{{mapper}}.{token}.{{library_name}}"
prefix = f"work/{infix}/log/{infix}.sv_calling"
key_ext = (
("log", ".log"),
("conda_info", ".conda_info.txt"),
Expand Down
203 changes: 103 additions & 100 deletions snappy_pipeline/workflows/sv_calling_wgs/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,13 @@ from snappy_pipeline.workflows.sv_calling_wgs import SvCallingWgsWorkflow
__author__ = "Manuel Holtgrewe <[email protected]>"


# Configuration ===============================================================
# Regular expression for wildcard constraints
RE_BETWEEN_DOTS = r"[^.\.]+"

# Configuration ===============================================================

configfile: "config.yaml"


# Expand "$ref" JSON pointers in configuration (also works for YAML)
config, lookup_paths, config_paths = expand_ref("config.yaml", config)

Expand Down Expand Up @@ -200,91 +201,93 @@ rule sv_calling_wgs_delly2_merge_genotypes:
# wf.wrapper_path("sniffles2/germline/snf_to_vcf")


## PopDel Steps ----------------------------------------------------------------
#
#
# ruleorder: sv_calling_wgs_popdel_reorder_vcf > sv_calling_wgs_popdel_concat_calls > sv_calling_wgs_popdel_call > sv_calling_wgs_popdel_profile
#
#
# rule sv_calling_wgs_popdel_profile:
# input:
# unpack(wf.get_input_files("popdel", "profile")),
# output:
# **wf.get_output_files("popdel", "profile"),
# threads: wf.get_resource("popdel", "profile", "threads")
# resources:
# time=wf.get_resource("popdel", "profile", "time"),
# memory=wf.get_resource("popdel", "profile", "memory"),
# partition=wf.get_resource("popdel", "profile", "partition"),
# tmpdir=wf.get_resource("popdel", "profile", "tmpdir"),
# wildcard_constraints:
# index_ngs_library=r"[^\.]+",
# log:
# **wf.get_log_file("popdel", "profile"),
# wrapper:
# wf.wrapper_path("popdel/profile")
#
#
# rule sv_calling_wgs_popdel_call:
# input:
# unpack(wf.get_input_files("popdel", "call")),
# output:
# **wf.get_output_files("popdel", "call"),
# threads: wf.get_resource("popdel", "call", "threads")
# resources:
# time=wf.get_resource("popdel", "call", "time"),
# memory=wf.get_resource("popdel", "call", "memory"),
# partition=wf.get_resource("popdel", "call", "partition"),
# tmpdir=wf.get_resource("popdel", "call", "tmpdir"),
# log:
# **wf.get_log_file("popdel", "call"),
# wrapper:
# wf.wrapper_path("popdel/call")
#
#
# rule sv_calling_wgs_popdel_concat_calls:
# input:
# unpack(wf.get_input_files("popdel", "concat_calls")),
# output:
# **wf.get_output_files("popdel", "concat_calls"),
# threads: wf.get_resource("popdel", "concat_calls", "threads")
# resources:
# time=wf.get_resource("popdel", "concat_calls", "time"),
# memory=wf.get_resource("popdel", "concat_calls", "memory"),
# partition=wf.get_resource("popdel", "concat_calls", "partition"),
# tmpdir=wf.get_resource("popdel", "concat_calls", "tmpdir"),
# log:
# **wf.get_log_file("popdel", "concat_calls"),
# wrapper:
# wf.wrapper_path("popdel/concat_calls")
#
#
# rule sv_calling_wgs_popdel_reorder_vcf:
# input:
# unpack(wf.get_input_files("popdel", "reorder_vcf")),
# output:
# **wf.get_output_files("popdel", "reorder_vcf"),
# threads: wf.get_resource("popdel", "reorder_vcf", "threads")
# resources:
# time=wf.get_resource("popdel", "reorder_vcf", "time"),
# memory=wf.get_resource("popdel", "reorder_vcf", "memory"),
# partition=wf.get_resource("popdel", "reorder_vcf", "partition"),
# tmpdir=wf.get_resource("popdel", "reorder_vcf", "tmpdir"),
# wildcard_constraints:
# index_ngs_library=r"[^\.]+",
# params:
# ped_members=wf.substep_getattr("popdel", "get_ped_members"),
# log:
# **wf.get_log_file("popdel", "reorder_vcf"),
# wrapper:
# wf.wrapper_path("popdel/reorder_vcf")
# PopDel Steps ----------------------------------------------------------------


# Run Melt --------------------------------------------------------------------
rule sv_calling_wgs_popdel_profile:
input:
unpack(wf.get_input_files("popdel", "profile")),
output:
**wf.get_output_files("popdel", "profile"),
wildcard_constraints:
mapper=RE_BETWEEN_DOTS,
index_ngs_library=RE_BETWEEN_DOTS,
threads: wf.get_resource("popdel", "profile", "threads")
resources:
time=wf.get_resource("popdel", "profile", "time"),
memory=wf.get_resource("popdel", "profile", "memory"),
partition=wf.get_resource("popdel", "profile", "partition"),
tmpdir=wf.get_resource("popdel", "profile", "tmpdir"),
log:
**wf.get_log_file("popdel", "profile"),
wrapper:
wf.wrapper_path("popdel/profile")


# Regular expression for wildcard constraints
RE_NO_DOT = r"[^.]+"
rule sv_calling_wgs_popdel_call:
input:
unpack(wf.get_input_files("popdel", "call")),
output:
**wf.get_output_files("popdel", "call"),
wildcard_constraints:
mapper=RE_BETWEEN_DOTS,
chrom=RE_BETWEEN_DOTS,
begin=RE_BETWEEN_DOTS,
end=RE_BETWEEN_DOTS,
threads: wf.get_resource("popdel", "call", "threads")
resources:
time=wf.get_resource("popdel", "call", "time"),
memory=wf.get_resource("popdel", "call", "memory"),
partition=wf.get_resource("popdel", "call", "partition"),
tmpdir=wf.get_resource("popdel", "call", "tmpdir"),
log:
**wf.get_log_file("popdel", "call"),
wrapper:
wf.wrapper_path("popdel/call")


rule sv_calling_wgs_popdel_concat_calls:
input:
unpack(wf.get_input_files("popdel", "concat_calls")),
output:
**wf.get_output_files("popdel", "concat_calls"),
wildcard_constraints:
mapper=RE_BETWEEN_DOTS,
threads: wf.get_resource("popdel", "concat_calls", "threads")
resources:
time=wf.get_resource("popdel", "concat_calls", "time"),
memory=wf.get_resource("popdel", "concat_calls", "memory"),
partition=wf.get_resource("popdel", "concat_calls", "partition"),
tmpdir=wf.get_resource("popdel", "concat_calls", "tmpdir"),
log:
**wf.get_log_file("popdel", "concat_calls"),
wrapper:
wf.wrapper_path("popdel/concat_calls")


rule sv_calling_wgs_popdel_reorder_vcf:
input:
unpack(wf.get_input_files("popdel", "reorder_vcf")),
output:
**wf.get_output_files("popdel", "reorder_vcf"),
wildcard_constraints:
mapper=RE_BETWEEN_DOTS,
index_ngs_library=RE_BETWEEN_DOTS,
threads: wf.get_resource("popdel", "reorder_vcf", "threads")
resources:
time=wf.get_resource("popdel", "reorder_vcf", "time"),
memory=wf.get_resource("popdel", "reorder_vcf", "memory"),
partition=wf.get_resource("popdel", "reorder_vcf", "partition"),
tmpdir=wf.get_resource("popdel", "reorder_vcf", "tmpdir"),
params:
ped_members=wf.substep_getattr("popdel", "get_ped_members"),
log:
**wf.get_log_file("popdel", "reorder_vcf"),
wrapper:
wf.wrapper_path("popdel/reorder_vcf")


# Run Melt --------------------------------------------------------------------


rule sv_calling_wgs_melt_preprocess:
Expand All @@ -293,9 +296,9 @@ rule sv_calling_wgs_melt_preprocess:
output:
**wf.get_output_files("melt", "preprocess"),
wildcard_constraints:
mapper=RE_NO_DOT,
library_name=RE_NO_DOT,
me_type=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
library_name=RE_BETWEEN_DOTS,
me_type=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "preprocess", "threads")
resources:
time=wf.get_resource("melt", "preprocess", "time"),
Expand All @@ -315,9 +318,9 @@ rule sv_calling_wgs_melt_indiv_analysis:
output:
**wf.get_output_files("melt", "indiv_analysis"),
wildcard_constraints:
mapper=RE_NO_DOT,
library_name=RE_NO_DOT,
me_type=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
library_name=RE_BETWEEN_DOTS,
me_type=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "indiv_analysis", "threads")
resources:
time=wf.get_resource("melt", "indiv_analysis", "time"),
Expand All @@ -337,9 +340,9 @@ rule sv_calling_wgs_melt_group_analysis:
output:
**wf.get_output_files("melt", "group_analysis"),
wildcard_constraints:
mapper=RE_NO_DOT,
index_library_name=RE_NO_DOT,
me_type=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
index_library_name=RE_BETWEEN_DOTS,
me_type=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "group_analysis", "threads")
resources:
time=wf.get_resource("melt", "group_analysis", "time"),
Expand All @@ -359,9 +362,9 @@ rule sv_calling_wgs_melt_genotype:
output:
**wf.get_output_files("melt", "genotype"),
wildcard_constraints:
mapper=RE_NO_DOT,
index_library_name=RE_NO_DOT,
me_type=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
index_library_name=RE_BETWEEN_DOTS,
me_type=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "genotype", "threads")
resources:
time=wf.get_resource("melt", "genotype", "time"),
Expand All @@ -381,8 +384,8 @@ rule sv_calling_wgs_melt_make_vcf:
output:
**wf.get_output_files("melt", "make_vcf"),
wildcard_constraints:
mapper=RE_NO_DOT,
index_library_name=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
index_library_name=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "make_vcf", "threads")
resources:
time=wf.get_resource("melt", "make_vcf", "time"),
Expand All @@ -402,8 +405,8 @@ rule sv_calling_wgs_melt_merge_vcf:
output:
**wf.get_output_files("melt", "merge_vcf"),
wildcard_constraints:
mapper=RE_NO_DOT,
library_name=RE_NO_DOT,
mapper=RE_BETWEEN_DOTS,
library_name=RE_BETWEEN_DOTS,
threads: wf.get_resource("melt", "merge_vcf", "threads")
resources:
time=wf.get_resource("melt", "merge_vcf", "time"),
Expand Down Expand Up @@ -434,7 +437,7 @@ rule sv_calling_wgs_gcnv_preprocess_intervals:
log:
wf.get_log_file("gcnv", "preprocess_intervals"),
wrapper:
wf.wrapper_path("gcnv/preprocess_intervals")
wf.wrapper_path("gcnv/preprocess_intervals_wgs")


rule sv_calling_wgs_gcnv_coverage:
Expand Down
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