remove remaining enable_conda, use conda.enabled in workflow

nf-core · Dec 22, 2022 · 32e5345 · 32e5345
1 parent 7e2d27f
commit 32e5345
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Showing 5 changed files with 6 additions and 4 deletions.
diff --git a/modules/local/external_tools_import.nf b/modules/local/external_tools_import.nf
@@ -4,7 +4,7 @@
 process EXTERNAL_TOOLS_IMPORT {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
+    conda "conda-forge::coreutils=9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"

diff --git a/modules/local/get_prediction_versions.nf b/modules/local/get_prediction_versions.nf
@@ -1,7 +1,7 @@
 process GET_PREDICTION_VERSIONS {
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::epytope=3.1.0" : null)
+    conda "bioconda::epytope=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/epytope:3.1.0--pyh5e36f6f_0' :
         'quay.io/biocontainers/epytope:3.1.0--pyh5e36f6f_0' }"

diff --git a/modules/local/merge_json.nf b/modules/local/merge_json.nf
@@ -1,7 +1,7 @@
 process MERGE_JSON {
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
+    conda "conda-forge::python=3.8.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/python:3.8.3' :
         'quay.io/biocontainers/python:3.8.3' }"

diff --git a/nextflow.config b/nextflow.config
@@ -80,6 +80,8 @@ params {
     config_profile_url         = null
     config_profile_name        = null
 
+    conda.enabled = false
+
     // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'

diff --git a/workflows/epitopeprediction.nf b/workflows/epitopeprediction.nf
@@ -150,7 +150,7 @@ workflow EPITOPEPREDICTION {
 
     if (tools.isEmpty()) { exit 1, "No valid tools specified." }
 
-    if (params.enable_conda && params.tools.contains("netmhc")) {
+    if (params.conda.enabled && params.tools.contains("netmhc")) {
             log.warn("Please note: if you want to use external prediction tools with conda it might be necessary to set --netmhc_system to darwin depending on your system.")
     }