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Remove 'defaults' conda channel from docs. #5607

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merged 3 commits into from
Dec 16, 2024
Merged

Remove 'defaults' conda channel from docs. #5607

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be25b17
Remove 'defaults' conda channel from docs.
ewels Dec 13, 2024
94e845c
Merge branch 'master' into docs-no-defaults
bentsherman Dec 13, 2024
b25862c
Update hashes in tests
ewels Dec 16, 2024
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4 changes: 2 additions & 2 deletions docs/conda.md
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,6 @@ name: my-env
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- star=2.5.4a
- bwa=0.7.15
Expand Down Expand Up @@ -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:
Expand Down
12 changes: 6 additions & 6 deletions modules/nextflow/src/test/groovy/nextflow/conda/CondaCacheTest.groovy
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Expand Up @@ -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:
Expand All @@ -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)

Expand All @@ -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
Expand Down
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