fix some conda declarations

Author: nvnieuwk

modules/local/bcftools/consensus_reheader/environment.yml

@@ -2,6 +2,5 @@ name: bcftools_annotate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.17

modules/local/bcftools/split_by_svtype/environment.yml

@@ -2,6 +2,5 @@ name: bcftools_annotate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bcftools=1.17

…dules/local/fix_callers/environment.yaml modules/local/fix_callers/environment.ymlmodules/local/fix_callers/environment.yaml renamed to modules/local/fix_callers/environment.yml modules/local/fix_callers/environment.yaml renamed to modules/local/fix_callers/environment.yml

@@ -2,7 +2,6 @@ name: python-tabix
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::tabix
   - conda-forge::python=3.12

modules/local/fix_callers/main.nf

@@ -2,6 +2,7 @@ process FIX_CALLERS {
     tag "$meta.id"
     label 'process_low'
 
+    conda "${moduleDir}/environment.yml"
     container "quay.io/cmgg/python-tabix:0.0.1"
 
     input:

tests/default.nf.test.snap

@@ -189,7 +189,7 @@
                 "PosCon2.vcf.gz,variantsMD5:96649c806adcbe582972f575141762bc",
                 "PosCon2.vcf.gz,variantsMD5:3f0cef0b03989a61774515c2388665a",
                 "PosCon2.vcf.gz,variantsMD5:d41d8cd98f00b204e9800998ecf8427e",
-                "PosCon3.vcf.gz,variantsMD5:cccbd2438a85041a2b5419532f3d90b4",
+                "PosCon3.vcf.gz,variantsMD5:d1a07a2cf16b5245b574bfaac6898ea8",
                 "PosCon3.vcf.gz,variantsMD5:cdfb36aca0449e97c71386056070a11b",
                 "PosCon3.vcf.gz,variantsMD5:96649c806adcbe582972f575141762bc",
                 "PosCon3.vcf.gz,variantsMD5:e2076228968e4150616e5a4a12f2326a",
@@ -206,6 +206,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-12T10:28:50.304470336"
+        "timestamp": "2026-01-12T16:55:47.317560351"
     }
 }