Merge pull request #551 from maxulysse/nf_core_sentieon_license

FEAT: Add software_license profile

.github/workflows/main.yml

@@ -107,6 +107,7 @@ jobs:
           - "scw"
           - "seawulf"
           - "seg_globe"
+          - "software_license"
           - "tigem"
           - "tubingen_apg"
           - "tuos_stanage"

conf/software_license.config

@@ -0,0 +1,18 @@
+//Profile config names for nf-core/configs
+params {
+    config_profile_description = 'Software license set up for nf-core by nf-core/configs'
+    config_profile_contact = 'Maxime U Garcia (@maxulysse)'
+    config_profile_url = 'https://nf-co.re'
+    sentieon_extension = null
+
+    validationSchemaIgnoreParams = "cf_ploidy,genomes,sentieon_extension,test_data"
+}
+
+if (params.sentieon_extension) {
+    process {
+        withLabel: 'sentieon' {
+            ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 ?: ''
+            ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 ?: ''
+        }
+    }
+}

docs/software_license.md

@@ -0,0 +1,5 @@
+# nf-core/configs: Software licenses set up for nf-core
+
+To use, run the pipeline with `-profile software_license`. This will download and launch
+the [`software_license.config`](../conf/software_license.config) which has been pre-configured with a
+setup suitable for using _Sentieon_ within the nf-core GHA.

nfcore_custom.config

@@ -85,10 +85,11 @@ profiles {
     rosalind_uge     { includeConfig "${params.custom_config_base}/conf/rosalind_uge.config" }
     sage             { includeConfig "${params.custom_config_base}/conf/sage.config" }
     sahmri           { includeConfig "${params.custom_config_base}/conf/sahmri.config" }
-    sanger           { includeConfig "${params.custom_config_base}/conf/sanger.config"}    
+    sanger           { includeConfig "${params.custom_config_base}/conf/sanger.config"}
     scw              { includeConfig "${params.custom_config_base}/conf/scw.config"}
     seawulf          { includeConfig "${params.custom_config_base}/conf/seawulf.config"}
     seg_globe        { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
+    software_license { includeConfig "${params.custom_config_base}/conf/software_license.config"}
     tigem            { includeConfig "${params.custom_config_base}/conf/tigem.config"}
     tubingen_apg     { includeConfig "${params.custom_config_base}/conf/tubingen_apg.config" }
     tuos_stanage     { includeConfig "${params.custom_config_base}/conf/tuos_stanage.config"}