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Update 20231121 #257

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merged 3 commits into from
Nov 21, 2023
Merged

Update 20231121 #257

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aa9c6ec
Update nextflow.config to update version
erinyoung Nov 21, 2023
523e309
Update freyja.nf to version 1.4.7-2023-11-21
erinyoung Nov 21, 2023
5d2a3ee
Update samtools to 1.18
erinyoung Nov 21, 2023
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8 changes: 4 additions & 4 deletions modules/freyja.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process freyja_variants {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-14'
container 'quay.io/uphl/freyja:1.4.7-2023-11-21'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -44,7 +44,7 @@ process freyja_demix {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-14'
container 'quay.io/uphl/freyja:1.4.7-2023-11-21'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -85,7 +85,7 @@ process freyja_boot {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-14'
container 'quay.io/uphl/freyja:1.4.7-2023-11-21'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -124,7 +124,7 @@ process freyja_aggregate {
tag "Aggregating results from freyja"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'quay.io/uphl/freyja:1.4.7-2023-11-14'
container 'quay.io/uphl/freyja:1.4.7-2023-11-21'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down
20 changes: 10 additions & 10 deletions modules/samtools.nf
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Expand Up @@ -2,7 +2,7 @@ process samtools_stats {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -37,7 +37,7 @@ process samtools_coverage {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -74,7 +74,7 @@ process samtools_flagstat {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -111,7 +111,7 @@ process samtools_depth {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -147,7 +147,7 @@ process samtools_ampliconstats {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -185,7 +185,7 @@ process samtools_plot_ampliconstats {
label "process_single"
errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -221,7 +221,7 @@ process samtools_sort {
tag "${sample}"
label "process_high"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -258,7 +258,7 @@ process samtools_filter {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -300,7 +300,7 @@ process samtools_ampliconclip {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down Expand Up @@ -340,7 +340,7 @@ process samtools_markdup {
tag "${sample}"
label "process_single"
publishDir "${params.outdir}", mode: 'copy'
container 'staphb/samtools:1.17'
container 'staphb/samtools:1.18'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ manifest {
name = 'Cecret'
author = 'Erin Young'
homePage = 'https://github.com/UPHL-BioNGS/Cecret'
version = 'v3.10.20231115'
version = 'v3.10.20231121'
defaultBranch = 'master'
recurseSubmodules = false
description = 'Reference-based consensus creation'
Expand Down