conf

Author: famosab

nextflow.config

@@ -174,9 +174,6 @@ profiles {
     test { includeConfig 'conf/test.config' }
 }
 
-// Load qbic-pipelines/vcftomaf custom profiles from different institutions.
-// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/vcftomaf.config" : "/dev/null"
-
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
@@ -186,16 +183,15 @@ podman.registry       = 'quay.io'
 singularity.registry  = 'quay.io'
 charliecloud.registry = 'quay.io'
 
-// Load nf-core custom profiles from different institutions
-includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE')|| !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
+// Load nf-core custom profiles from different institutions                                                                                                                 │
+includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load igenomes.config if required
 includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
-
 env {
     PYTHONNOUSERSITE = 1
     R_PROFILE_USER   = "/.Rprofile"