Remove 'defaults' conda channel from docs.

Fixes #5601 Signed-off-by: Phil Ewels <[email protected]>
nextflow-io · Dec 13, 2024 · be25b17 · be25b17
1 parent fc63128
commit be25b17
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/docs/conda.md b/docs/conda.md
@@ -72,7 +72,6 @@ name: my-env
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - star=2.5.4a
   - bwa=0.7.15
@@ -105,7 +104,8 @@ Conda environment files can also be used to install Python packages from the [Py
 ```yaml
 name: my-env-2
 channels:
-  - defaults
+  - conda-forge
+  - bioconda
 dependencies:
   - pip
   - pip:

diff --git a/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy b/modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
@@ -92,12 +92,12 @@ class CondaCacheTest extends Specification {
         def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
             channels:
+              - conda-forge
               - bioconda
-              - defaults
             dependencies:
               # Default bismark
               - star=2.5.4a
-              - bwa=0.7.15        
+              - bwa=0.7.15
             '''
             .stripIndent(true)  // https://issues.apache.org/jira/browse/GROOVY-9423
         when:
@@ -119,15 +119,15 @@ class CondaCacheTest extends Specification {
         def BASE = Paths.get('/conda/envs')
         def ENV = Files.createTempFile('test','.yml')
         def hash = CondaCache.sipHash(ENV)
-        ENV.text = '''  
+        ENV.text = '''
             name: my-env-1.1
             channels:
+              - conda-forge
               - bioconda
-              - defaults
             dependencies:
               # Default bismark
               - star=2.5.4a
-              - bwa=0.7.15        
+              - bwa=0.7.15
             '''
                 .stripIndent(true)
 
@@ -150,7 +150,7 @@ class CondaCacheTest extends Specification {
         def hash = CondaCache.sipHash(ENV)
         ENV.text = '''
                 star=2.5.4a
-                bwa=0.7.15   
+                bwa=0.7.15
                 multiqc=1.2.3
                 '''
                 .stripIndent(true)  // https://issues.apache.org/jira/browse/GROOVY-9423