From 9d421979b3ae83b184104f150fcdbec44c8273c2 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Tue, 12 Mar 2024 11:45:24 -0600 Subject: [PATCH] added saveAs --- modules/local/heatcluster.nf | 2 +- modules/local/iqtree2.nf | 2 +- modules/local/mash.nf | 6 +++--- modules/local/mashtree.nf | 2 +- modules/local/multiqc.nf | 2 +- modules/local/mykrobe.nf | 2 +- modules/local/panaroo.nf | 4 ++-- modules/local/pbptyper.nf | 2 +- modules/local/phytreeviz.nf | 4 ++-- modules/local/plasmidfinder.nf | 2 +- modules/local/prokka.nf | 2 +- modules/local/quast.nf | 2 +- 12 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/local/heatcluster.nf b/modules/local/heatcluster.nf index 72269cf..9958c92 100755 --- a/modules/local/heatcluster.nf +++ b/modules/local/heatcluster.nf @@ -1,7 +1,7 @@ process heatcluster { tag "HeatCluster" label "process_single" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/heatcluster:1.0.2c' time '10m' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/iqtree2.nf b/modules/local/iqtree2.nf index 8556926..d1ad8f3 100644 --- a/modules/local/iqtree2.nf +++ b/modules/local/iqtree2.nf @@ -1,7 +1,7 @@ process iqtree2 { tag "Phylogenetic analysis" label "process_high" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/iqtree2:2.2.2.7' time '24h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/mash.nf b/modules/local/mash.nf index 4d71d75..c90a31b 100644 --- a/modules/local/mash.nf +++ b/modules/local/mash.nf @@ -1,7 +1,7 @@ process mash_sketch_fastq { tag "${meta.id}" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/mash:2.3' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10m' @@ -41,7 +41,7 @@ process mash_sketch_fastq { process mash_sketch_fasta { tag "${meta.id}" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/mash:2.3' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10m' @@ -80,7 +80,7 @@ process mash_sketch_fasta { process mash_dist { tag "${meta.id}" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/mash:2.3' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10m' diff --git a/modules/local/mashtree.nf b/modules/local/mashtree.nf index 420064e..c7223ec 100755 --- a/modules/local/mashtree.nf +++ b/modules/local/mashtree.nf @@ -1,7 +1,7 @@ process mashtree { tag "Phylogenetic analysis" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/mashtree:1.4.6' stageInMode 'copy' time '4h' diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf index 1b06f93..6bd2bfc 100644 --- a/modules/local/multiqc.nf +++ b/modules/local/multiqc.nf @@ -41,7 +41,7 @@ process multiqc { process versions { tag "extracting versions" label "process_single" - publishDir "${params.outdir}/summary", mode: 'copy' + // no publishDir container 'staphb/multiqc:1.19' time '10m' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/mykrobe.nf b/modules/local/mykrobe.nf index a322877..5a4d757 100644 --- a/modules/local/mykrobe.nf +++ b/modules/local/mykrobe.nf @@ -2,7 +2,7 @@ process mykrobe { tag "${meta.id}" label "process_medium" stageInMode "copy" - publishDir path: params.outdir, mode: 'copy' + publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/mykrobe:0.13.0' time '1h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/panaroo.nf b/modules/local/panaroo.nf index 6caaa56..21477c4 100755 --- a/modules/local/panaroo.nf +++ b/modules/local/panaroo.nf @@ -1,7 +1,7 @@ process panaroo { tag "Core Genome Alignment" label "process_high" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/panaroo:1.3.4' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} time '10h' @@ -11,7 +11,7 @@ process panaroo { output: path "panaroo/*" , emit: files - tuple path("panaroo/core_gene_alignment.aln"), path("panaroo/gene_presence_absence.Rtab"), emit: core_gene_alignment + tuple path("panaroo/core_gene_alignment.aln"), path("panaroo/gene_presence_absence.Rtab"), emit: core_gene_alignment, optional: true path "logs/${task.process}/*.log" , emit: log_files path "versions.yml" , emit: versions diff --git a/modules/local/pbptyper.nf b/modules/local/pbptyper.nf index 179b82f..97e8aea 100644 --- a/modules/local/pbptyper.nf +++ b/modules/local/pbptyper.nf @@ -2,7 +2,7 @@ process pbptyper { tag "${meta.id}" label "process_medium" stageInMode "copy" - publishDir path: params.outdir, mode: 'copy' + publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/pbptyper:1.0.4' time '1h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/phytreeviz.nf b/modules/local/phytreeviz.nf index 8324559..e557296 100755 --- a/modules/local/phytreeviz.nf +++ b/modules/local/phytreeviz.nf @@ -1,8 +1,8 @@ process phytreeviz { tag "${analysis}" label "process_medium" - publishDir params.outdir, mode: 'copy' - container 'staphb/phytreeviz:0.1.0' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + container 'staphb/phytreeviz:0.2.0' time '1h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/plasmidfinder.nf b/modules/local/plasmidfinder.nf index 3e28218..767beb3 100644 --- a/modules/local/plasmidfinder.nf +++ b/modules/local/plasmidfinder.nf @@ -1,7 +1,7 @@ process plasmidfinder { tag "${meta.id}" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/plasmidfinder:2.1.6' time '10m' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/prokka.nf b/modules/local/prokka.nf index 4c22a0e..e3eec08 100644 --- a/modules/local/prokka.nf +++ b/modules/local/prokka.nf @@ -1,7 +1,7 @@ process prokka { tag "${meta.id}" label "process_high" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/prokka:1.14.6' time '2h' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} diff --git a/modules/local/quast.nf b/modules/local/quast.nf index 736b7e3..f20af34 100644 --- a/modules/local/quast.nf +++ b/modules/local/quast.nf @@ -1,7 +1,7 @@ process quast { tag "${meta.id}" label "process_medium" - publishDir params.outdir, mode: 'copy' + publishDir params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } container 'staphb/quast:5.2.0' time '10m' errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}