uncommented errorstrategy

UPHL-BioNGS · Feb 13, 2024 · f45d9e6 · f45d9e6
1 parent 9408d6d
commit f45d9e6
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Showing 25 changed files with 37 additions and 40 deletions.
diff --git a/modules/local/amrfinderplus.nf b/modules/local/amrfinderplus.nf
@@ -3,7 +3,7 @@ process amrfinderplus {
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/ncbi-amrfinderplus:3.11.26-2023-11-15.1'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time '10m'
 
   input:

diff --git a/modules/local/bbduk.nf b/modules/local/bbduk.nf
@@ -3,7 +3,7 @@ process bbduk {
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/bbtools:39.01'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:

diff --git a/modules/local/drprg.nf b/modules/local/drprg.nf
@@ -5,7 +5,7 @@ process drprg {
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/drprg:0.1.1'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(flag)

diff --git a/modules/local/elgato.nf b/modules/local/elgato.nf
@@ -4,7 +4,7 @@ process elgato {
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/elgato:1.15.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(flag)

diff --git a/modules/local/emmtyper.nf b/modules/local/emmtyper.nf
@@ -5,7 +5,7 @@ process emmtyper {
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/emmtyper:0.2.0'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   when:
   (task.ext.when == null || task.ext.when) && flag =~ 'found'

diff --git a/modules/local/fastani.nf b/modules/local/fastani.nf
@@ -6,7 +6,7 @@ process fastani {
   publishDir    path: params.outdir, mode: 'copy', pattern: 'fastani/*' 
   container     'staphb/fastani:1.34'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), file(genomes)

diff --git a/modules/local/heatcluster.nf b/modules/local/heatcluster.nf
@@ -4,7 +4,7 @@ process heatcluster {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/heatcluster:1.0.2c'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(matrix)

diff --git a/modules/local/iqtree2.nf b/modules/local/iqtree2.nf
@@ -4,7 +4,7 @@ process iqtree2 {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/iqtree2:2.2.2.7'
   time          '24h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(msa)

diff --git a/modules/local/kaptive.nf b/modules/local/kaptive.nf
@@ -5,7 +5,7 @@ process kaptive {
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/kaptive:2.0.8'
   time          '30m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(flag)

diff --git a/modules/local/kleborate.nf b/modules/local/kleborate.nf
@@ -4,7 +4,7 @@ process kleborate {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/kleborate:2.4.1'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contig), val(flag), file(script)

diff --git a/modules/local/local.nf b/modules/local/local.nf
@@ -5,7 +5,7 @@ process core_genome_evaluation {
   publishDir  path: params.outdir, mode: 'copy', pattern: 'core_genome_evaluation/core_genome_evaluation.csv'
   container   'quay.io/biocontainers/pandas:1.5.2'
   time        '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple file(fasta), file(summary), file(script)
@@ -32,10 +32,10 @@ process core_genome_evaluation {
 process flag {
   tag           "${meta.id}"
   label         "process_single"
-  //publishDir    params.outdir, mode: 'copy'
+  //no publishDir    params.outdir, mode: 'copy'
   container     'quay.io/biocontainers/pandas:1.5.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(files)
@@ -139,7 +139,7 @@ process json_convert {
   // no publishDir
   container 'quay.io/biocontainers/pandas:1.5.2'
   time      '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), val(analysis), file(json), file(script)
@@ -163,7 +163,7 @@ process mash_err {
   label         "process_single"
   container     'quay.io/biocontainers/pandas:1.5.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(error_file)
@@ -192,7 +192,7 @@ process mqc_prep {
   label         "process_single"
   container     'quay.io/biocontainers/pandas:1.5.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(input)
@@ -216,7 +216,7 @@ process names {
   label         "process_single"
   container     'quay.io/biocontainers/pandas:1.5.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(input)
@@ -244,7 +244,7 @@ process references {
   label     "process_single"
   container 'quay.io/uphl/grandeur_ref:20240124'
   time      '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   output:
   path "ref/*", emit: fastas
@@ -266,7 +266,7 @@ process species {
   publishDir    params.outdir, mode: 'copy'
   container     'quay.io/biocontainers/pandas:1.5.2'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(results)
@@ -306,7 +306,7 @@ process summary {
   container     'quay.io/biocontainers/pandas:1.5.2'
   label         "process_single"
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(input)

diff --git a/modules/local/mashtree.nf b/modules/local/mashtree.nf
@@ -5,7 +5,7 @@ process mashtree {
   container     'staphb/mashtree:1.4.6'
   stageInMode 'copy'
   time      '4h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(assemblies)

diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
@@ -4,7 +4,7 @@ process multiqc {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/multiqc:1.19'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(input)
@@ -44,7 +44,7 @@ process versions {
   publishDir    "${params.outdir}/summary", mode: 'copy'
   container     'staphb/multiqc:1.19'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(input)

diff --git a/modules/local/mykrobe.nf b/modules/local/mykrobe.nf
@@ -4,8 +4,8 @@ process mykrobe {
   stageInMode   "copy"
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/mykrobe:0.13.0'
-  time      '1h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  time          '1h'
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(flag)

diff --git a/modules/local/panaroo.nf b/modules/local/panaroo.nf
@@ -3,7 +3,7 @@ process panaroo {
   label         "process_high"
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/panaroo:1.3.4'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time '10h'
 
   input:

diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf
@@ -5,7 +5,7 @@ process pbptyper {
   publishDir    path: params.outdir, mode: 'copy'
   container     'staphb/pbptyper:1.0.4'
   time          '1h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(flag)

diff --git a/modules/local/phytreeviz.nf b/modules/local/phytreeviz.nf
@@ -4,7 +4,7 @@ process phytreeviz {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/phytreeviz:0.1.0'
   time          '1h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(analysis), file(newick)

diff --git a/modules/local/plasmidfinder.nf b/modules/local/plasmidfinder.nf
@@ -4,7 +4,7 @@ process plasmidfinder {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/plasmidfinder:2.1.6'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(file), file(script)

diff --git a/modules/local/prokka.nf b/modules/local/prokka.nf
@@ -4,7 +4,7 @@ process prokka {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/prokka:1.14.6'
   time          '2h'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs), val(organism)

diff --git a/modules/local/quast.nf b/modules/local/quast.nf
@@ -4,7 +4,7 @@ process quast {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/quast:5.2.0'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(contigs)

diff --git a/modules/local/roary.nf b/modules/local/roary.nf
@@ -3,7 +3,7 @@ process roary {
   label         "process_high"
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/roary:3.13.0'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10h'
 
   input:

diff --git a/modules/local/seqsero2.nf b/modules/local/seqsero2.nf
@@ -4,7 +4,7 @@ process seqsero2 {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/seqsero2:1.2.1'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   tuple val(meta), file(file), val(flag)

diff --git a/modules/local/serotypefinder.nf b/modules/local/serotypefinder.nf
@@ -5,7 +5,7 @@ process serotypefinder {
   container     'staphb/serotypefinder:2.0.1'
   maxForks      10
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}  
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}  
 
   input:
   tuple val(meta), file(file), val(flag), file(script)

diff --git a/modules/local/shigatyper.nf b/modules/local/shigatyper.nf
@@ -4,7 +4,7 @@ process shigatyper {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/shigatyper:2.0.5'
   stageInMode   'copy'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:

diff --git a/modules/local/snp-dists.nf b/modules/local/snp-dists.nf
@@ -4,11 +4,8 @@ process snp_dists {
   publishDir    params.outdir, mode: 'copy'
   container     'staphb/snp-dists:0.8.2'
   maxForks      10
-  //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-  //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
-  //#UPHLICA memory 1.GB
-  //#UPHLICA cpus 3
-  //#UPHLICA time '24h'
+  time          '2h'
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(contigs)