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Merge pull request #415 from jfy133/tsv-input
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Re-add accidently removed nf-core config profile loading
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jfy133 authored May 12, 2020
2 parents 8a6bde0 + 82fd8c5 commit c82adb1
Showing 1 changed file with 9 additions and 3 deletions.
12 changes: 9 additions & 3 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -209,7 +209,7 @@ params {
awsregion = 'eu-west-1'
igenomes_ignore = false
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}/"
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = false
config_profile_description = false
config_profile_contact = false
Expand All @@ -229,7 +229,14 @@ process.container = 'nfcore/eager:dev'
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

// Load nf-core/eager custom profiles from different Institutions
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load nf-core/eager custom profiles from different institutions
try {
includeConfig "${params.custom_config_base}/pipeline/eager.config"
} catch (Exception e) {
Expand All @@ -256,7 +263,6 @@ profiles {


profiles {
awsbatch { includeConfig 'conf/awsbatch.config'}
conda { process.conda = "$baseDir/environment.yml"}
debug { process.beforeScript = 'echo $HOSTNAME'}
docker {
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