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Pcgr project tracking #62

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Merged
MareikeJaniak merged 8 commits into from
Oct 28, 2025
Merged

Pcgr project tracking #62

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a698814
testing export of timestamp variable to prevent restarts
MareikeJaniak Oct 27, 2025
65da90d
testing export of timestamp variable to prevent restarts
MareikeJaniak Oct 27, 2025
d2a2d43
testing export of timestamp variable to prevent restarts
MareikeJaniak Oct 27, 2025
2757d04
Changing timestamp to env var to patch auto restart
paulstretenowich Oct 27, 2025
959e861
formatting
MareikeJaniak Oct 28, 2025
446cbfd
fix for kallisto adding other options twice, error introduced by Mare…
MareikeJaniak Oct 28, 2025
93eb394
fix input dependencies for cnvkit_batch cna
MareikeJaniak Oct 28, 2025
917cbbc
change shebang line in prologue and epilogue to prevent python versio…
MareikeJaniak Oct 28, 2025
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2 changes: 1 addition & 1 deletion genpipes/core/epilogue.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.12.2/bin/python
#!/usr/bin/env python

import csv
import os
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2 changes: 1 addition & 1 deletion genpipes/core/prologue.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/cvmfs/soft.mugqic/CentOS6/software/python/Python-3.12.2/bin/python
#!/usr/bin/env python

import csv
import os
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4 changes: 3 additions & 1 deletion genpipes/core/scheduler.py
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Expand Up @@ -333,14 +333,16 @@ def job2json_project_tracking(self, pipeline, job, job_status):
-j \\"{job_name}\\" \\{metrics}
-o \\"{json_outfile}\\" \\
-f {status}
export PT_JSON_OUTFILE=\\"{json_outfile}\\" {command_separator}
export PT_JSON_OUTFILE=\\"{json_outfile}\\"
export TIMESTAMP=\\"{timestamp}\\" {command_separator}
""".format(
job2json_project_tracking_script="genpipes tools job2json_project_tracking",
samples=",".join([sample.name for sample in job.samples]),
readsets=",".join([readset.name for readset in job.readsets]),
job_name=job.name,
metrics=('\n -m \\"' + ','.join(job.metrics) + '\\" \\') if job.metrics else '',
json_outfile=json_outfile,
timestamp=pipeline.timestamp,
status=job_status,
command_separator="&&" if (job_status=='\\"RUNNING\\"') else ""
) if json_outfile else ""
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8 changes: 4 additions & 4 deletions genpipes/pipelines/dnaseq/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2822,7 +2822,7 @@ def report_pcgr(self):

if self.project_tracking_json:
samples = [sample]
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_{self.timestamp}.o")
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_$TIMESTAMP.o")
jobs.append(
concat_jobs(
[
Expand Down Expand Up @@ -2960,7 +2960,7 @@ def report_pcgr(self):
samples = [tumor_pair.normal, tumor_pair.tumor]

if self.project_tracking_json:
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_{self.timestamp}.o")
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_$TIMESTAMP.o")
jobs.append(
concat_jobs(
[
Expand Down Expand Up @@ -3958,7 +3958,7 @@ def cnvkit_batch(self):
name=f"cnvkit_batch.cna.{sample_name}",
samples=samples,
readsets=readsets,
input_dependency=[input_cna, output_cna],
input_dependency=[input_cna],
output_dependency=[header, output_cna_body, output_cna]
)
)
Expand Down Expand Up @@ -4197,7 +4197,7 @@ def cnvkit_batch(self):
name=f"cnvkit_batch.cna.{sample_name}",
samples=[tumor_pair.normal, tumor_pair.tumor],
readsets=[*list(tumor_pair.normal.readsets), *list(tumor_pair.tumor.readsets)],
input_dependency=[input_cna, output_cna],
input_dependency=[input_cna],
output_dependency=[header, output_cna_body, output_cna],
removable_files=[header, output_cna_body]
)
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4 changes: 2 additions & 2 deletions genpipes/pipelines/longread_dnaseq/__init__.py
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Expand Up @@ -1911,7 +1911,7 @@ def report_pcgr(self):

if self.project_tracking_json:
samples = [sample]
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_{self.timestamp}.o")
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_$TIMESTAMP.o")
jobs.append(
concat_jobs(
[
Expand Down Expand Up @@ -2024,7 +2024,7 @@ def report_pcgr(self):
samples = [tumor_pair.normal, tumor_pair.tumor]

if self.project_tracking_json:
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_{self.timestamp}.o")
pcgr_output_file = os.path.join(self.output_dir, "job_output", "report_pcgr", f"{job_name}_$TIMESTAMP.o")
jobs.append(
concat_jobs(
[
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2 changes: 1 addition & 1 deletion genpipes/pipelines/rnaseq_light/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ def kallisto(self):
transcriptome_file = global_conf.global_get('kallisto', 'transcriptome_idx', param_type="filepath")
tx2genes_file = global_conf.global_get('kallisto', 'transcript2genes', param_type="filepath")
bootstraps = global_conf.global_get('kallisto', 'bootstraps')
other_param = global_conf.global_get('kallisto', 'other_options', required=False)
other_param = global_conf.global_get('kallisto', 'other_parameters', required=False)

jobs = []

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