skip concoct due to excess in timelimt

Daniel-VM · Sep 5, 2024 · 6549160 · 6549160
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commit 6549160
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Showing 2 changed files with 9 additions and 8 deletions.
diff --git a/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog b/bu_isciii/templates/mag/ANALYSIS/ANALYSIS03_MAG_ALL/lablog
@@ -30,6 +30,7 @@ nextflow run /data/bi/pipelines/nf-core-mag/nf-core-mag-2.5.3/workflow/main.nf \
     --input samplesheet.csv \\
     --kraken2_db '/data/bi/references/kraken/minikraken_8GB_20200312.tgz' \\
     --skip_spadeshybrid true \\
+    --skip_concoct true \\
     --refine_bins_dastool true \\
     --outdir $(date '+%Y%m%d')_mag_all \\
     -resume

diff --git a/bu_isciii/templates/mag/DOC/mag.config b/bu_isciii/templates/mag/DOC/mag.config
@@ -28,14 +28,14 @@ process {
 		errorStrategy = { task.exitStatus in [ 1, 255 ] ? 'ignore' : 'retry' }
 		time          = { 8.h * task.attempt }
 	}
-	// TODO: This bining tool takes ~24h to finish... Consider skipping it.  
-	withName:'CONCOCT_CONCOCT' {
-		errorStrategy = { task.exitStatus in [140] ? 'retry' : 'finish' }
-		maxRetries = 2
-		cpus = { 8 * task.attempt }
-		memory = { 64.GB * task.attempt }
-		time = { 24.h * task.attempt }
-	}
+	// TODO: This bining tool takes ~24h to finish... skip was added in lablog, however it can be enabeled.
+	// withName:'CONCOCT_CONCOCT' {
+	// 	errorStrategy = { task.exitStatus in [140] ? 'retry' : 'finish' }
+	// 	maxRetries = 2
+	// 	cpus = { 8 * task.attempt }
+	// 	memory = { 64.GB * task.attempt }
+	// 	time = { 24.h * task.attempt }
+	// }
 	withName:'CHECKM_LINEAGEWF' {
 		errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' }
                 maxRetries = 3