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feat: implement suspect data workflow flags for #22 #73

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Merged
crashfrog merged 7 commits into from
May 29, 2026
Merged

feat: implement suspect data workflow flags for #22 #73

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bfcc4c6
test: add acceptance tests for #22
crashfrog May 27, 2026
68d7df6
feat: implement suspect data workflow flags for #22
crashfrog May 27, 2026
d1d0ae5
Merge main: combine strategy and suspect data flags
crashfrog May 29, 2026
5e5ca00
Update test fixture to use builtin workflow
crashfrog May 29, 2026
2149989
Implement quality.json filtering in workflows
crashfrog May 29, 2026
060f82c
Fix test parameter names to match balanced_typing workflow
crashfrog May 29, 2026
23e7eeb
Mark miniwdl integration tests with @pytest.mark.miniwdl
crashfrog May 29, 2026
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17 changes: 16 additions & 1 deletion torchbase/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -204,9 +204,14 @@ def _strategy_callback(ctx, param, value):
@ReadsParam("-pe2", "--paired2", "--pe2")
@ReadsParam("-i", "--interlaced")
@ReadsParam("-l", "--longreads")
@click.option("--quality-json", type=click.Path(exists=True), default=None, help="Quality JSON file for suspect data filtering")
@click.option("--include-suspect-alleles", "allele_filter", flag_value="include", default=True, help="Include suspect alleles (default)")
@click.option("--exclude-suspect-alleles", "allele_filter", flag_value="exclude", help="Exclude suspect alleles")
@click.option("--exclude-suspect-loci", is_flag=True, default=False, help="Exclude suspect loci")
@click.option("--exclude-suspect-profiles", is_flag=True, default=False, help="Exclude suspect profiles")
@click.argument('torch_args', nargs=-1, type=click.UNPROCESSED)
@click.pass_context
def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=None, strategy='balanced', contigs=None, reads=None, paired1=None, paired2=None, interlaced=None, longreads=None, torch_args=[]):
def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=None, strategy='balanced', contigs=None, reads=None, paired1=None, paired2=None, interlaced=None, longreads=None, quality_json=None, allele_filter="include", exclude_suspect_loci=False, exclude_suspect_profiles=False, torch_args=[]):
"Run the selected torch."
from torchbase.torchfs import Torch
from torchbase.registry import RegistryManager
Expand Down Expand Up @@ -307,6 +312,16 @@ def _run(clx, torch, cromwell_options="", method="main", workflow=None, output=N
if longreads:
miniwdl_cmd.extend(['longreads=' + str(longreads)])

# Add quality.json and suspect data flags
if quality_json:
miniwdl_cmd.extend(['quality_json=' + str(quality_json)])
if allele_filter == "exclude":
miniwdl_cmd.append('exclude_suspect_alleles=true')
if exclude_suspect_loci:
miniwdl_cmd.append('exclude_suspect_loci=true')
if exclude_suspect_profiles:
miniwdl_cmd.append('exclude_suspect_profiles=true')

# Execute workflow
result = run(miniwdl_cmd)

Expand Down
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