Merge pull request #8 from gagnonanthony/dev

hotfix module parameters update when using profiles
scilus · Jan 7, 2025 · 6c88eb4 · 6c88eb4
2 parents e689d05 + e5bc08e
commit 6c88eb4
Showing 1 changed file with 3 additions and 13 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -255,9 +255,6 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
 profiles {
     debug {
         dumpHashes              = true
@@ -387,26 +384,16 @@ profiles {
     }
     infant {
         params.infant                           = true
-
         params.dwi_run_synthstrip               = true
-
         params.dwi_normalize_fa_mask_threshold  = 0.10
-
-        //params.fodf_max_fa_threshold            = 0.01
-        //params.fodf_min_md_threshold            = 0.00185
-
         params.frf_manual_frf                   = "12,5,5"
-
         params.run_pft_tracking                 = false
         params.local_min_len                    = 15
         params.local_fa_seeding_mask_threshold  = 0.10
-
         params.commit_para_diff                 = "1.2E-3"
         params.commit_iso_diff                  = "2.0E-3"
-
         params.decompose_min_len                = 10
         params.decompose_outlier_threshold      = 0.4
-
     }
     tracking {
         params.tracking         = true
@@ -419,6 +406,9 @@ profiles {
     }
 }
 
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+
 // Load nf-core custom profiles from different Institutions
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"