added saveAs

UPHL-BioNGS · Mar 12, 2024 · 08574e4 · 08574e4
1 parent f0c4cd3
commit 08574e4
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Showing 15 changed files with 17 additions and 17 deletions.
diff --git a/modules/local/bbduk.nf b/modules/local/bbduk.nf
@@ -1,7 +1,7 @@
 process bbduk {
   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/bbtools:39.01'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'

diff --git a/modules/local/blast.nf b/modules/local/blast.nf
@@ -1,7 +1,7 @@
 process blastn {
   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/blast:2.15.0'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '2h'

diff --git a/modules/local/blobtools.nf b/modules/local/blobtools.nf
@@ -1,7 +1,7 @@
 process blobtools_create {
   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     'chrishah/blobtools:v1.1.1'
   time          '45m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -41,7 +41,7 @@ process blobtools_create {
 
 process blobtools_view {
   tag           "${meta.id}"
-  publishDir    params.outdir, mode: 'copy'
+  publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'chrishah/blobtools:v1.1.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
@@ -78,7 +78,7 @@ process blobtools_view {
 
 process blobtools_plot {
   tag           "${meta.id}"
-  publishDir    params.outdir, mode: 'copy'
+  publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'chrishah/blobtools:v1.1.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/datasets.nf b/modules/local/datasets.nf
@@ -1,7 +1,7 @@
 process datasets_summary {
   tag           "${taxon}"
   label         "process_single"
-  publishDir    params.outdir, mode: 'copy'
+  publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'staphb/ncbi-datasets:16.2.0'
   time          '1h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore' }

diff --git a/modules/local/drprg.nf b/modules/local/drprg.nf
@@ -2,7 +2,7 @@ process drprg {
   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/drprg:0.1.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/elgato.nf b/modules/local/elgato.nf
@@ -1,7 +1,7 @@
 process elgato {
   tag           "${meta.id}"
   label         "process_medium"
-  publishDir    path: params.outdir, mode: 'copy'
+  publishDir    path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'staphb/elgato:1.15.2'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/emmtyper.nf b/modules/local/emmtyper.nf
@@ -2,7 +2,7 @@ process emmtyper {
   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/emmtyper:0.2.0'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/kaptive.nf b/modules/local/kaptive.nf
@@ -2,7 +2,7 @@ process kaptive {
   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/kaptive:2.0.8'
   time          '30m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/kleborate.nf b/modules/local/kleborate.nf
@@ -1,7 +1,7 @@
 process kleborate {
   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/kleborate:2.4.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/kraken2.nf b/modules/local/kraken2.nf
@@ -1,7 +1,7 @@
 process kraken2 {
   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/kraken2:2.1.3'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '1h'

diff --git a/modules/local/seqsero2.nf b/modules/local/seqsero2.nf
@@ -1,7 +1,7 @@
 process seqsero2 {
   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/seqsero2:1.2.1'
   time          '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/serotypefinder.nf b/modules/local/serotypefinder.nf
@@ -1,7 +1,7 @@
 process serotypefinder {
   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/serotypefinder:2.0.1'
   maxForks      10
   time          '10m'

diff --git a/modules/local/shigatyper.nf b/modules/local/shigatyper.nf
@@ -1,7 +1,7 @@
 process shigatyper {
   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/shigatyper:2.0.5'
   stageInMode   'copy'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}

diff --git a/modules/local/snp-dists.nf b/modules/local/snp-dists.nf
@@ -1,7 +1,7 @@
 process snp_dists {
   tag           "SNP matrix"
   label         "process_medium"
-  publishDir    params.outdir, mode: 'copy'
+  publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'staphb/snp-dists:0.8.2'
   maxForks      10
   time          '2h'

diff --git a/modules/local/spades.nf b/modules/local/spades.nf
@@ -1,7 +1,7 @@
 process spades {
   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/spades:3.15.5'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '5h'