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Save sample/patient-specific metapipeline logs #196

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merged 8 commits into from
May 10, 2024
Merged

Save sample/patient-specific metapipeline logs #196

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827e503
added patient specific metapipeline trace, timeline and report
zhuchcn Apr 4, 2024
b0ac628
fix (module/nextflow.config): unknown attribute trace.metapipeline_lo…
zhuchcn Apr 4, 2024
c5d0b89
move sample/patient-specific metapipelien log to metapipeline_DNA_bas…
zhuchcn May 6, 2024
c3041ce
changelog updated
zhuchcn May 6, 2024
165e505
add task hash to nextflow log dir name
zhuchcn May 7, 2024
d9942ee
get task hash from work dir
zhuchcn May 7, 2024
c445490
--task-hash to --task_hash
zhuchcn May 7, 2024
51d75c9
Update CHANGELOG.md
zhuchcn May 10, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
+ More descriptive error messages on failure to identify output files
+ Add call-sCNA to `requested_pipelines` in `template.config`
+ Handling for SRC inputs
+ Save nextflow logs sample/patient-specific metapipeline. #187
### Changed
+ Use GitHub container registry CI/CD check
+ Calculate-targeted-coverage: `1.0.0-rc.2` -> `1.1.0`
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15 changes: 15 additions & 0 deletions config/metapipeline_DNA_base.config
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Expand Up @@ -3,3 +3,18 @@ process {
ext.fail_gracefully = true
}
}

trace {
enabled = true
file = "${params.metapipeline_log_output_dir}/nextflow-log/${params.patient}-${params.task_hash}/trace.txt"
}

report {
enabled = true
file = "${params.metapipeline_log_output_dir}/nextflow-log/${params.patient}-${params.task_hash}/report.html"
}

timeline {
enabled = true
file = "${params.metapipeline_log_output_dir}/nextflow-log/${params.patient}-${params.task_hash}/timeline.html"
}
3 changes: 3 additions & 0 deletions main.nf
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Expand Up @@ -193,6 +193,8 @@ process call_metapipeline_DNA {
: "\${CURRENT_WORK_DIR:=`pwd`}"
: "\${SBATCH_RET:=-1}"

task_hash=\$(pwd | rev | cut -d '/' -f 1,2 | rev | sed 's/\\//_/')

NXF_WORK=${params.resolved_work_dir} \
nextflow run \
${moduleDir}/module/metapipeline_DNA.nf \
Expand All @@ -213,6 +215,7 @@ process call_metapipeline_DNA {
--normal_sample_count ${params.sample_counts[patient]['normal']} \
--tumor_sample_count ${params.sample_counts[patient]['tumor']} \
--use_original_intervals ${params.use_original_intervals} \
--task_hash \${task_hash} \
-params-file ${pipeline_params_json} \
-c ${moduleDir}/config/metapipeline_DNA_base.config
""" + limiter_wrapper_post
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