Mega conda environment update: Remove name and defaults (#6600)

* Remove defaults channel from all modules

* Remove 'name' from conda environment files

* Update conda environment schema

* Remove defaults from env template and GHA CI

* Update Prettier in GHA test.yml workflow to match pre-commit version

* Remove whitespace from environment.yml files

.github/env-template.yml

@@ -1,4 +1,3 @@
 channels:
   - conda-forge
   - bioconda
-  - defaults

.github/workflows/test.yml

@@ -50,7 +50,7 @@ jobs:
           node-version: "20"
 
       - name: Install Prettier
-        run: npm install -g prettier@3.1.0
+        run: npm install -g prettier@3.2.5
 
       - name: Run Prettier --check
         run: prettier --check .
@@ -439,7 +439,7 @@ jobs:
         uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:
           miniconda-version: "latest"
-          channels: conda-forge,bioconda,defaults
+          channels: conda-forge,bioconda
           python-version: ${{ matrix.python-version }}
 
       - name: Conda setup
@@ -687,7 +687,7 @@ jobs:
         with:
           miniconda-version: "latest"
           auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
+          channels: conda-forge,bioconda
 
       - name: Conda setup
         if: matrix.profile == 'conda'

modules/environment-schema.json

@@ -4,10 +4,6 @@
     "description": "Validate the environment.yml file for an nf-core module",
     "type": "object",
     "properties": {
-        "name": {
-            "type": "string",
-            "description": "The name of the component, same as in the meta.yml"
-        },
         "channels": {
             "type": "array",
             "items": {
@@ -22,5 +18,6 @@
             }
         }
     },
-    "required": ["name", "channels", "dependencies"]
+    "required": ["channels", "dependencies"],
+    "not": { "required": ["name"] }
 }

modules/nf-core/abacas/environment.yml

@@ -1,7 +1,5 @@
-name: abacas
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::abacas=1.3.1

modules/nf-core/abricate/run/environment.yml

@@ -1,7 +1,5 @@
-name: abricate_run
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::abricate=1.0.1

modules/nf-core/abricate/summary/environment.yml

@@ -1,7 +1,5 @@
-name: abricate_summary
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::abricate=1.0.1

modules/nf-core/abritamr/run/environment.yml

@@ -1,7 +1,5 @@
-name: abritamr_run
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::abritamr=1.0.14

modules/nf-core/adapterremoval/environment.yml

@@ -1,7 +1,5 @@
-name: adapterremoval
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::adapterremoval=2.3.2

modules/nf-core/adapterremovalfixprefix/environment.yml

@@ -1,7 +1,5 @@
-name: adapterremovalfixprefix
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::adapterremovalfixprefix=0.0.5

modules/nf-core/admixture/environment.yml

@@ -1,7 +1,5 @@
-name: admixture
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::admixture=1.3.0

modules/nf-core/affy/justrma/environment.yml

@@ -1,8 +1,6 @@
-name: affy_justrma
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::bioconductor-affy=1.78.0
   - conda-forge::r-base=4.3.1

modules/nf-core/agat/convertspgff2gtf/environment.yml

@@ -1,7 +1,5 @@
-name: agat_convertspgff2gtf
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agat=1.4.0

modules/nf-core/agat/convertspgff2tsv/environment.yml

@@ -1,7 +1,5 @@
-name: agat_convertspgff2tsv
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agat=1.4.0

modules/nf-core/agat/convertspgxf2gxf/environment.yml

@@ -1,7 +1,5 @@
-name: agat_convertspgxf2gxf
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agat=1.4.0

modules/nf-core/agat/spaddintrons/environment.yml

@@ -1,7 +1,5 @@
-name: agat_spaddintrons
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::agat=1.4.0"

modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "agat_spfilterfeaturefromkilllist"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::agat=1.4.0"

modules/nf-core/agat/spmergeannotations/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "agat_spmergeannotations"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::agat=1.4.0"

modules/nf-core/agat/spstatistics/environment.yml

@@ -1,7 +1,5 @@
-name: agat_spstatistics
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agat=1.4.0

modules/nf-core/agat/sqstatbasic/environment.yml

@@ -1,7 +1,5 @@
-name: agat_sqstatbasic
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agat=1.4.0

modules/nf-core/agrvate/environment.yml

@@ -1,7 +1,5 @@
-name: agrvate
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::agrvate=1.0.2

modules/nf-core/ale/environment.yml

@@ -1,10 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "ale"
 channels:
   - conda-forge
   - bioconda
-  - defaults
   - tanghaibao
 dependencies:
   - "bioconda::ale=20180904"

modules/nf-core/allelecounter/environment.yml

@@ -1,7 +1,5 @@
-name: allelecounter
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::cancerit-allelecount=4.3.0

modules/nf-core/ampcombi/environment.yml

@@ -1,10 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "ampcombi"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::ampcombi=0.1.7
   - python=3.11

modules/nf-core/ampcombi2/cluster/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "ampcombi2_cluster"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::ampcombi=0.2.2"

modules/nf-core/ampcombi2/complete/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "ampcombi2_complete"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::ampcombi=0.2.2"

modules/nf-core/ampcombi2/parsetables/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "ampcombi2_parsetables"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::ampcombi=0.2.2"

modules/nf-core/ampir/environment.yml

@@ -1,7 +1,5 @@
-name: ampir
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::r-ampir=1.1.0

modules/nf-core/amplify/predict/environment.yml

@@ -1,7 +1,5 @@
-name: amplify_predict
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::amplify=2.0.0

modules/nf-core/amps/environment.yml

@@ -1,7 +1,5 @@
-name: amps
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hops=0.35

modules/nf-core/amrfinderplus/run/environment.yml

@@ -1,7 +1,5 @@
-name: amrfinderplus_run
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::ncbi-amrfinderplus=3.12.8

modules/nf-core/amrfinderplus/update/environment.yml

@@ -1,7 +1,5 @@
-name: amrfinderplus_update
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::ncbi-amrfinderplus=3.12.8

modules/nf-core/angsd/contamination/environment.yml

@@ -1,7 +1,5 @@
-name: angsd_contamination
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::angsd=0.940

modules/nf-core/angsd/docounts/environment.yml

@@ -1,7 +1,5 @@
-name: angsd_docounts
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::angsd=0.939

modules/nf-core/angsd/gl/environment.yml

@@ -1,10 +1,8 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "angsd_gl"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::angsd=0.940"
   - "bioconda::htslib=1.17"

modules/nf-core/annotsv/annotsv/environment.yml

@@ -1,7 +1,5 @@
-name: annotsv_annotsv
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::annotsv=3.4.2

modules/nf-core/annotsv/installannotations/environment.yml

@@ -1,7 +1,5 @@
-name: annotsv_installannotations
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::annotsv=3.4.2

modules/nf-core/anota2seq/anota2seqrun/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "anota2seq_anota2seqrun"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::bioconductor-anota2seq=1.24.0"

modules/nf-core/antismash/antismashlite/environment.yml

@@ -1,7 +1,5 @@
-name: antismash_antismashlite
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::antismash-lite=7.1.0

modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml

@@ -1,7 +1,5 @@
-name: antismash_antismashlitedownloaddatabases
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::antismash-lite=7.1.0

modules/nf-core/arcashla/extract/environment.yml

@@ -1,7 +1,5 @@
-name: arcashla_extract
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::arcas-hla=0.5.0

modules/nf-core/argnorm/environment.yml

@@ -1,7 +1,5 @@
-name: "argnorm"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "bioconda::argnorm=0.5.0"

modules/nf-core/aria2/environment.yml

@@ -1,7 +1,5 @@
-name: aria2
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - conda-forge::aria2=1.36.0

modules/nf-core/ariba/getref/environment.yml

@@ -1,7 +1,5 @@
-name: ariba_getref
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::ariba=2.14.6