added saveAs

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'}

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'}

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'

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'

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'}

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'}

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
 

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'}

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'}
 

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'}

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'}

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'}