diff --git a/donut_falls.nf b/donut_falls.nf index 75b8cbf..efdf2ca 100755 --- a/donut_falls.nf +++ b/donut_falls.nf @@ -162,7 +162,7 @@ process busco { tag "${meta.id}" label "process_medium" publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/busco:5.7.1-prok-bacteria_odb10_2024-01-08' + container 'staphb/busco:5.8.0-prok-bacteria_odb10_2024-01-08' time '45m' input: @@ -197,7 +197,7 @@ process bwa { tag "${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: @@ -275,7 +275,7 @@ process copy { tag "${meta.id}" label 'process_low' publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/multiqc:1.19' + container 'staphb/multiqc:1.25' time '10m' input: @@ -399,7 +399,7 @@ process dnaapler { tag "${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: @@ -498,7 +498,7 @@ process flye { tag "${meta.id}" label "process_high" publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/flye:2.9.4' + container 'staphb/flye:2.9.5' time '10h' input: @@ -588,7 +588,7 @@ process gfa_to_fasta { tag "${meta.id}" label "process_low" // no publishDir - container 'staphb/multiqc:1.19' + container 'staphb/multiqc:1.25' time '10m' input: @@ -740,7 +740,7 @@ process multiqc { tag "combining reports" label "process_low" publishDir "${params.outdir}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/multiqc:1.19' + container 'staphb/multiqc:1.25' time '10m' input: @@ -996,7 +996,7 @@ process png { tag "${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: @@ -1160,7 +1160,7 @@ process rasusa { tag "${meta.id}" label "process_medium" publishDir "${params.outdir}/${meta.id}", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/rasusa:2.0.0' + container 'staphb/rasusa:2.1.0' time '10m' input: @@ -1234,7 +1234,7 @@ process summary { tag "Creating summary" label "process_low" publishDir "${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: @@ -1548,7 +1548,7 @@ process versions { tag "extracting versions" label "process_low" publishDir "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/multiqc:1.19' + container 'staphb/multiqc:1.25' time '30m' input: @@ -1656,7 +1656,7 @@ process test { tag "Downloading R10.4 reads" label "process_low" publishDir "${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: @@ -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' }") -} \ No newline at end of file +}