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Merge pull request #182 from UPHL-BioNGS/update-20240306
Update 20240306
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,31 +1,181 @@ | ||
| process { | ||
| maxRetries = 0 | ||
| maxErrors = '-1' | ||
|
|
||
| withLabel:process_single { | ||
| cpus = { 1 } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 10.m * task.attempt } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 2.h * task.attempt } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| maxRetries = 0 | ||
| maxErrors = '-1' | ||
| withLabel:process_single { | ||
| cpus = { 1 } | ||
| memory = { 6.GB * task.attempt } | ||
| time = { 10.m * task.attempt } | ||
| } | ||
| withLabel:process_low { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 2.h * task.attempt } | ||
| } | ||
| withLabel:process_medium { | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 4.h * task.attempt } | ||
| } | ||
| withLabel:process_high { | ||
| cpus = { 2 * task.attempt } | ||
| cpus = { 2 * task.attempt } | ||
| memory = { 12.GB * task.attempt } | ||
| time = { 16.h * task.attempt } | ||
| } | ||
| withLabel:process_long { | ||
| time = { 20.h * task.attempt } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { 12.GB * task.attempt } | ||
| } | ||
| } | ||
| } | ||
| withLabel:process_high_memory { | ||
| memory = { 12.GB * task.attempt } | ||
| } | ||
|
|
||
| withName:amrfinderplus { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:bbduk { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:blastn { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:blobtools_create { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:blobtools_plot { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:blobtools_view { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:circulocov { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:core_genome_evaluation { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:datasets_download { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:datasets_summary { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:download_sra { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:drprg { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:elgato { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:emmtyper { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:fastani { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:fastp { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:fastqc { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:flag { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:heatcluster { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:iqtree2 { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:json_convert { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:kaptive { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:kleborate { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:kraken2 { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mash_dist { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mash_err { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mash_sketch_fasta { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mash_sketch_fastq { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mashtree { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mlst { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mqc_prep { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:multiqc { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:mykrobe { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:names { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:panaroo { | ||
| publishDir = [ path: "grandeur", mode: 'link', pattern: "panaroo/*"] | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:pbptyper { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:phytreeviz { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:plasmidfinder { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:prokka { | ||
| publishDir = [ path: "grandeur", mode: 'link', pattern: "gff/*.gff" ] | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:quast { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:references { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:seqsero2 { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:serotypefinder { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:shigatyper { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:snp_dists { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:spades { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:species { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:summary { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| withName:versions { | ||
| errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} | ||
| } | ||
| } |
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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