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Update 20231219 #163

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Merged
merged 6 commits into from
Dec 19, 2023
Merged

Update 20231219 #163

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365d33f
Changed to pandas
erinyoung Dec 19, 2023
3993b42
Update datasets to 15.34.0-2023-12-19
erinyoung Dec 19, 2023
0b97ae4
Update heatcluster to version 1.0.2
erinyoung Dec 19, 2023
275adf5
Version Bump
erinyoung Dec 19, 2023
026a4d5
Fixed typo
erinyoung Dec 19, 2023
7067823
Fixed typo
erinyoung Dec 19, 2023
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4 changes: 2 additions & 2 deletions modules/datasets.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process datasets_summary {
tag "${taxon}"
publishDir params.outdir, mode: 'copy'
container 'quay.io/uphl/datasets:15.31.1-2023-12-05'
container 'quay.io/uphl/datasets:15.34.0-2023-12-19'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
Expand Down Expand Up @@ -39,7 +39,7 @@ process datasets_download {
// because there's no way to specify threads
label "medcpus"
publishDir = [ path: "${params.outdir}", mode: 'copy', pattern: "logs/*/*log" ]
container 'quay.io/uphl/datasets:15.31.1-2023-12-05'
container 'quay.io/uphl/datasets:15.34.0-2023-12-19'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
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4 changes: 2 additions & 2 deletions modules/grandeur.nf
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Expand Up @@ -209,7 +209,7 @@ process names {
process size {
tag "${sample}"
publishDir params.outdir, mode: 'copy'
container 'quay.io/uphl/seaborn:0.12.2-2'
container 'quay.io/biocontainers/pandas:1.5.2'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
Expand Down Expand Up @@ -431,4 +431,4 @@ process summary {

python summary.py | tee -a $log_file
'''
}
}
2 changes: 1 addition & 1 deletion modules/heatcluster.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process heatcluster {
tag "HeatCluster"
publishDir params.outdir, mode: 'copy'
container 'quay.io/uphl/heatcluster:0.4.13-2023-12-05'
container 'quay.io/uphl/heatcluster:1.0.2-2023-12-19'
maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-medium'
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2 changes: 1 addition & 1 deletion modules/iqtree2.nf
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@@ -1,5 +1,5 @@
process iqtree2 {
tag "Pylogenetic Analysis"
tag "Phylogenetic analysis"
label "maxcpus"
publishDir params.outdir, mode: 'copy'
container 'staphb/iqtree2:2.2.2.6'
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4 changes: 2 additions & 2 deletions modules/mashtree.nf
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
process mashtree {
tag "Pylogenetic Analysis"
tag "Phylogenetic analysis"
label "maxcpus"
publishDir params.outdir, mode: 'copy'
container 'staphb/mashtree:1.2.0'
Expand Down Expand Up @@ -36,4 +36,4 @@ process mashtree {
--outtree mashtree/mashtree.nwk \
| tee -a $log_file
'''
}
}
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -3,7 +3,7 @@ manifest {
author = 'Erin Young'
homePage = 'https://github.com/UPHL-BioNGS/Grandeur'
mainScript = 'grandeur.nf'
version = '3.6.20231205'
version = '3.6.20231219'
defaultBranch = 'main'
description = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
}
Expand Down