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v1.5.0 - find summary .txt file id #28

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merged 5 commits into from
Jun 28, 2024
Merged

v1.5.0 - find summary .txt file id #28

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96c654c
add code to find summary .txt file id
growland2 Jun 27, 2024
854a9e5
fix for if no summary file
growland2 Jun 28, 2024
e8b385e
summary file to None if not present
growland2 Jun 28, 2024
785c113
small fix
growland2 Jun 28, 2024
70c9b08
remove try/except for summary file
growland2 Jun 28, 2024
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14 changes: 11 additions & 3 deletions src/eggd_artemis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ def find_snv_files(reports):
{
'SNV variant report': 'file-ZX',
'Coverage report': {'$dnanexus_link': 'file-GH'},
'Summary text file': 'file-NM',
'SNV count': 1
}
],
Expand All @@ -50,6 +51,7 @@ def find_snv_files(reports):
{
'SNV variant report': 'file-GH',
'Coverage report': {'$dnanexus_link': 'file-GH'},
'Summary text file': 'file-JK',
'SNV count': 3
}
]
Expand Down Expand Up @@ -98,8 +100,13 @@ def _find(report):
except KeyError:
coverage_report = parent_details["output"]["stage-Fyq5z18433GfYZbp3vX1KqjB.report"]

summary_text = parent_details.get("output", {}).get("stage-rpt_athena.summary_text", {}).get("$dnanexus_link")
if not summary_text:
print(f"No summary .txt file found in output of eggd_athena stage"
f" for SNV reports workflow ({parent_details})")

# Extract the sention job id from the vcf metadata
sention_job_id=dxpy.describe(vcf_file)["createdBy"]["job"]
sention_job_id = dxpy.describe(vcf_file)["createdBy"]["job"]
sentieon_details = dxpy.bindings.dxjob.DXJob(dxid=sention_job_id).describe()

# Get bam & bai job id from sention job metadata
Expand All @@ -117,6 +124,7 @@ def _find(report):
{
"SNV variant report": report['describe']['id'],
"Coverage report": coverage_report,
"Summary text file": summary_text,
"SNV count": str(snv_variant_count)
}
]
Expand Down Expand Up @@ -411,10 +419,10 @@ def get_multiqc_report(path_to_reports, project):
multiqc_file (str): file id of the multiqc file
"""
# Get path to single from reports path
single=f"/output/{path_to_reports.split('/')[2]}"
single = f"/output/{path_to_reports.split('/')[2]}"

# Find MultiQC jobs in the project
multiqc_reports=list(dxpy.bindings.search.find_jobs(
multiqc_reports = list(dxpy.bindings.search.find_jobs(
name_mode='glob',
name="*MultiQC*",
state="done",
Expand Down