drop custom labels for generic nf-core labels

bactopia · Apr 6, 2023 · 9d01454 · 9d01454
1 parent 3c8fd12
commit 9d01454
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Showing 10 changed files with 8 additions and 346 deletions.
diff --git a/modules/local/bactopia/assembler/main.nf b/modules/local/bactopia/assembler/main.nf
@@ -10,7 +10,7 @@ conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.c
 
 process ASSEMBLER {
     tag "${meta.id}"
-    label "max_cpu_75"
+    label "process_low"
     label "assemble_genome"
 
     conda (params.enable_conda ? conda_env : null)

diff --git a/modules/local/bactopia/datasets/main.nf b/modules/local/bactopia/datasets/main.nf
@@ -6,6 +6,7 @@ conda_name  = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env   = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
 process DATASETS {
+    label "process_low"
     storeDir params.datasets_cache
     publishDir params.datasets_cache
 

diff --git a/modules/local/bactopia/gather/main.nf b/modules/local/bactopia/gather/main.nf
@@ -10,7 +10,9 @@ conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.c
 
 process GATHER {
     tag "${meta.id}"
-    label "gather_samples"
+    label "process_low"
+    maxForks params.max_downloads
+    maxRetries params.max_retry
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?

diff --git a/modules/local/bactopia/qc/main.nf b/modules/local/bactopia/qc/main.nf
@@ -10,8 +10,7 @@ conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.c
 
 process QC {
     tag "${meta.id}"
-    label "base_mem_4gb"
-    label "qc_reads"
+    label "process_low"
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?

diff --git a/modules/local/bactopia/sketcher/main.nf b/modules/local/bactopia/sketcher/main.nf
@@ -10,8 +10,7 @@ conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.c
 
 process SKETCHER {
     tag "${meta.id}"
-    label "base_mem_8gb"
-    label "minmer_sketch"
+    label "process_low"
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?

diff --git a/modules/local/teton/kraken2_bracken/main.nf b/modules/local/teton/kraken2_bracken/main.nf
diff --git a/modules/local/teton/kraken2_bracken/meta.yml b/modules/local/teton/kraken2_bracken/meta.yml
diff --git a/modules/local/teton/kraken2_bracken/params.config b/modules/local/teton/kraken2_bracken/params.config
diff --git a/modules/local/teton/kraken2_bracken/params.json b/modules/local/teton/kraken2_bracken/params.json
diff --git a/subworkflows/local/bracken/main.nf b/subworkflows/local/bracken/main.nf
@@ -22,7 +22,7 @@ options.args2 = [
 ].join(' ').replaceAll("\\s{2,}", " ").trim()
 DATABASE = params.kraken2_db ? file(params.kraken2_db) : []
 
-include { KRAKEN2_BRACKEN as KRAKEN2_BRACKEN_MODULE } from '../../../modules/local/teton/kraken2_bracken/main' addParams( options: options )
+include { BRACKEN as BRACKEN_MODULE } from '../../../modules/nf-core/bracken/main' addParams( options: options )
 
 workflow BRACKEN {
     take: