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Update donut_falls to latest software versions #99

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merged 4 commits into from
Nov 7, 2024
Merged

Update donut_falls to latest software versions #99

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d666070
Update donut_falls to latest software versions
erinyoung Nov 5, 2024
0d8b74f
Update all of the other instances of multiqc
erinyoung Nov 5, 2024
9b116ff
Changes container from multiqc to gfastats for wget
erinyoung Nov 5, 2024
4408358
Update busco to 5.8.0-prok-bacteria_odb10_2024-01-08
erinyoung Nov 5, 2024
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26 changes: 13 additions & 13 deletions donut_falls.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ process busco {
tag "${meta.id}"
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/busco:5.7.1-prok-bacteria_odb10_2024-01-08'
container 'staphb/busco:5.8.0-prok-bacteria_odb10_2024-01-08'
time '45m'

input:
Expand Down Expand Up @@ -197,7 +197,7 @@ process bwa {
tag "${meta.id}"
label 'process_high'
// no publishDir because the sam files are too big
container 'staphb/bwa:0.7.17'
container 'staphb/bwa:0.7.18'
time '2h'

input:
Expand Down Expand Up @@ -275,7 +275,7 @@ process copy {
tag "${meta.id}"
label 'process_low'
publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '10m'

input:
Expand Down Expand Up @@ -399,7 +399,7 @@ process dnaapler {
tag "${meta.id}"
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/dnaapler:0.7.0'
container 'staphb/dnaapler:0.8.1'
time '1h'

input:
Expand Down Expand Up @@ -498,7 +498,7 @@ process flye {
tag "${meta.id}"
label "process_high"
publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/flye:2.9.4'
container 'staphb/flye:2.9.5'
time '10h'

input:
Expand Down Expand Up @@ -588,7 +588,7 @@ process gfa_to_fasta {
tag "${meta.id}"
label "process_low"
// no publishDir
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '10m'

input:
Expand Down Expand Up @@ -740,7 +740,7 @@ process multiqc {
tag "combining reports"
label "process_low"
publishDir "${params.outdir}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '10m'

input:
Expand Down Expand Up @@ -996,7 +996,7 @@ process png {
tag "${meta.id}"
label "process_low"
publishDir "${params.outdir}/${meta.id}/bandage", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '10m'

input:
Expand Down Expand Up @@ -1160,7 +1160,7 @@ process rasusa {
tag "${meta.id}"
label "process_medium"
publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/rasusa:2.0.0'
container 'staphb/rasusa:2.1.0'
time '10m'

input:
Expand Down Expand Up @@ -1234,7 +1234,7 @@ process summary {
tag "Creating summary"
label "process_low"
publishDir "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '30m'

input:
Expand Down Expand Up @@ -1548,7 +1548,7 @@ process versions {
tag "extracting versions"
label "process_low"
publishDir "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/multiqc:1.25'
time '30m'

input:
Expand Down Expand Up @@ -1656,7 +1656,7 @@ process test {
tag "Downloading R10.4 reads"
label "process_low"
publishDir "${params.outdir}/test_files/", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
container 'staphb/gfastats:1.3.7'
time '1h'

output:
Expand Down Expand Up @@ -1979,4 +1979,4 @@ workflow.onComplete {
println("The consensus fasta files can be found in ${params.outdir}/sample/consensus")
println("The fasta files are from each phase of assembly. polca > polypolish > medaka > unpolished")
println("Execution status: ${ workflow.success ? 'OK' : 'failed' }")
}
}