made profiles add execution reports to output

nf-core · Sep 11, 2023 · c91e4e0 · c91e4e0
1 parent 3fe4256
commit c91e4e0
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Showing 6 changed files with 64 additions and 201 deletions.
diff --git a/assets/main_report/01-identification.Rmd b/assets/main_report/01-identification.Rmd
@@ -50,7 +50,7 @@ sample_ids <- core_tree$tip.label[core_tree$tip.label %in% samp_meta$modified_id
 colnames(ani_matrix) <- gsub(colnames(ani_matrix), pattern = "[.-]", replacement = "_")
 rownames(ani_matrix) <- colnames(ani_matrix)
 group_ani <- ani_matrix[rownames(ani_matrix) %in% core_tree$tip.label, colnames(ani_matrix) %in% core_tree$tip.label]
-core_tree <- root(core_tree, names(which.min(colMeans(group_ani[sample_ids, ]))))
+#core_tree <- root(core_tree, names(which.min(colMeans(group_ani[sample_ids, ]))))
 
 # Set tip labels to taxon names for reference sequences
 # TODO: need a more reliable way to get IDs

diff --git a/assets/main_report/_main.Rmd b/assets/main_report/_main.Rmd
diff --git a/conf/test.config b/conf/test.config
@@ -22,3 +22,23 @@ params {
     input  = 'test/data/metadata_small.csv'
     outdir = 'test/output_small'
 }
+
+report {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/execution_report.html"
+    overwrite = true
+}
+
+timeline {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/timeline_report.html"
+    overwrite = true
+}
+
+trace {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/trace_report.tsv"
+    overwrite = true
+    fields    = "task_id,hash,native_id,process,tag,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,workdir,scratch,error_action"
+}
+
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/plantpathsurveil -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -23,3 +23,23 @@ params {
     input  = 'test/data/metadata_full.csv'
     outdir = 'test/output_full'
 }
+
+report {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/execution_report.html"
+    overwrite = true
+}
+
+timeline {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/timeline_report.html"
+    overwrite = true
+}
+
+trace {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/trace_report.tsv"
+    overwrite = true
+    fields    = "task_id,hash,native_id,process,tag,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,workdir,scratch,error_action"
+}
+
diff --git a/conf/test_medium.config b/conf/test_medium.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/plantpathsurveil -profile test_medium,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/pathogensurveillance -profile test_medium,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -24,3 +24,22 @@ params {
     outdir = 'test/output_medium'
 }
 
+report {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/execution_report.html"
+    overwrite = true
+}
+
+timeline {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/timeline_report.html"
+    overwrite = true
+}
+
+trace {
+    enabled   = true
+    file      = "${params.outdir}/pipeline_info/trace_report.tsv"
+    overwrite = true
+    fields    = "task_id,hash,native_id,process,tag,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt,workdir,scratch,error_action"
+}
+
diff --git a/workflows/pathogensurveillance.nf b/workflows/pathogensurveillance.nf
@@ -168,6 +168,8 @@ workflow PATHOGENSURVEILLANCE {
     CUSTOM_DUMPSOFTWAREVERSIONS (                                               
         ch_versions.unique().collect(sort:true)
     )
+
+    println "$workflow.manifest"
 
     // MultiQC
     //workflow_summary    = WorkflowPathogensurveillance.paramsSummaryMultiqc(workflow, summary_params)