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added in error strategy
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@erinyoung
erinyoung committed Mar 4, 2024
1 parent 7613204 commit 6193043
Showing 1 changed file with 31 additions and 31 deletions.
62 changes: 31 additions & 31 deletions donut_falls.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ ch_input_files
// label "process_medium"
// publishDir "${params.outdir}/${meta.id}", mode: 'copy'
// container 'staphb/ontime:0.2.3'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '45m'
//
// input:
Expand Down Expand Up @@ -173,7 +173,7 @@ ch_input_files
// label "process_high"
// publishDir "${params.outdir}/${meta.id}", mode: 'copy'
// container 'staphb/dragonflye:1.1.2'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '10h'
//
// input:
Expand Down Expand Up @@ -220,7 +220,7 @@ ch_input_files
// label "process_high"
// publishDir "${params.outdir}/${meta.id}", mode: 'copy'
// container 'quay.io/biocontainers/hybracter:0.6.0--pyhdfd78af_0'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '10h'
//
// input:
Expand Down Expand Up @@ -257,7 +257,7 @@ ch_input_files
// label "process_single"
// publishDir "${params.outdir}/test_files/nfcore", mode: 'copy'
// container 'staphb/multiqc:1.19'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '1h'

// output:
Expand All @@ -277,7 +277,7 @@ ch_input_files
// label "process_single"
// publishDir "${params.outdir}/test_files/great", mode: 'copy'
// container 'staphb/multiqc:1.19'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '1h'

// output:
Expand All @@ -301,7 +301,7 @@ ch_input_files
// label "process_single"
// publishDir "${params.outdir}/test_files/good", mode: 'copy'
// container 'staphb/multiqc:1.19'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '1h'

// output:
Expand All @@ -322,7 +322,7 @@ ch_input_files
// label "process_single"
// publishDir "${params.outdir}/test_files/mediocre", mode: 'copy'
// container 'staphb/multiqc:1.19'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '1h'

// output:
Expand All @@ -345,7 +345,7 @@ ch_input_files
// label "process_single"
// publishDir "${params.outdir}/test_files/bad", mode: 'copy'
// container 'staphb/multiqc:1.19'
// //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
// time '1h'

// output:
Expand Down Expand Up @@ -402,7 +402,7 @@ process bandage {
label "process_low"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -437,7 +437,7 @@ process busco {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/busco:5.6.1-prok-bacteria_odb10_2024-01-08'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '45m'

input:
Expand Down Expand Up @@ -473,7 +473,7 @@ process bwa {
label 'process_high'
// no publishDir because the sam files are too big
container 'staphb/bwa:0.7.17'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '2h'

input:
Expand Down Expand Up @@ -508,7 +508,7 @@ process circulocov {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'quay.io/uphl/circulocov:0.1.20240104-2024-02-21'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '1h'

input:
Expand Down Expand Up @@ -553,7 +553,7 @@ process copy {
label "process_single"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/multiqc:1.19'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -656,7 +656,7 @@ process dnaapler {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/dnaapler:0.7.0'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '1h'

input:
Expand Down Expand Up @@ -693,7 +693,7 @@ process fastp {
label "process_low"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/fastp:0.23.4'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -756,7 +756,7 @@ process flye {
label "process_high"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/flye:2.9.3'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10h'

input:
Expand Down Expand Up @@ -803,7 +803,7 @@ process gfastats {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy', pattern: 'gfastats/*'
container 'staphb/gfastats:1.3.6'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -847,7 +847,7 @@ process gfa_to_fasta {
label "process_low"
// no publishDir
container 'staphb/multiqc:1.19'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -907,7 +907,7 @@ process medaka {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'ontresearch/medaka:v1.11.3'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '30m'

input:
Expand Down Expand Up @@ -950,7 +950,7 @@ process multiqc {
label "process_low"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/multiqc:1.19'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -1140,7 +1140,7 @@ process nanoplot_summary {
label "process_low"
publishDir "${params.outdir}/summary", mode: 'copy'
container 'staphb/nanoplot:1.42.0'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -1178,7 +1178,7 @@ process nanoplot {
label "process_low"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/nanoplot:1.42.0'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -1222,7 +1222,7 @@ process polypolish {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/polypolish:0.6.0'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '45m'

input:
Expand Down Expand Up @@ -1268,7 +1268,7 @@ process pypolca {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/pypolca:0.3.1'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '30m'

input:
Expand Down Expand Up @@ -1324,7 +1324,7 @@ process rasusa {
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/rasusa:0.8.0'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -1359,7 +1359,7 @@ process raven {
label "process_high"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/raven:1.8.3'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10h'

input:
Expand Down Expand Up @@ -1398,7 +1398,7 @@ process summary {
label "process_single"
publishDir "${params.outdir}/summary", mode: 'copy'
container 'staphb/multiqc:1.19'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10m'

input:
Expand Down Expand Up @@ -1552,7 +1552,7 @@ process unicycler {
label "process_high"
publishDir "${params.outdir}/${meta.id}", mode: 'copy'
container 'staphb/unicycler:0.5.0'
////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '10h'

input:
Expand Down Expand Up @@ -1596,7 +1596,7 @@ 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)
Expand Down Expand Up @@ -1704,7 +1704,7 @@ process test_unicycler {
label "process_single"
publishDir "${params.outdir}/test_files/unicycler", mode: 'copy'
container 'staphb/multiqc:1.19'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '1h'

output:
Expand All @@ -1726,7 +1726,7 @@ process test_donut_falls {
label "process_single"
publishDir "${params.outdir}/test_files/df", mode: 'copy'
container 'staphb/multiqc:1.19'
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
time '1h'

output:
Expand Down

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