Merge pull request #196 from uclahs-cds/czhu-fix-trace

Save sample/patient-specific metapipeline logs

CHANGELOG.md

@@ -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`

config/metapipeline_DNA_base.config

@@ -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"
+}

main.nf

@@ -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 \
@@ -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