diff --git a/docs/conda.md b/docs/conda.md index 8c7405c1a4..22616e5516 100644 --- 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 index f6b7fac271..2609e5f45f 100644 --- 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: @@ -105,7 +105,7 @@ class CondaCacheTest extends Specification { then: 1 * cache.isYamlFilePath(ENV.toString()) 1 * cache.getCacheDir() >> BASE - prefix.toString() == "/conda/envs/env-${hash}-9416240708c49c4e627414b46a743664" + prefix.toString() == "/conda/envs/env-${hash}-64874f9dc9e7be788384bccef357a4f4" cleanup: folder?.deleteDir() @@ -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) @@ -136,7 +136,7 @@ class CondaCacheTest extends Specification { then: 1 * cache.isYamlFilePath(ENV.toString()) 1 * cache.getCacheDir() >> BASE - prefix.toString() == "/conda/envs/env-${hash}-e7fafe40ca966397a2c0d9bed7181aa7" + prefix.toString() == "/conda/envs/env-${hash}-5b5c72e839d0c7dcabb5d06607c205fc" } @@ -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 @@ -161,7 +161,7 @@ class CondaCacheTest extends Specification { 1 * cache.isYamlFilePath(ENV.toString()) 1 * cache.isTextFilePath(ENV.toString()) 1 * cache.getCacheDir() >> BASE - prefix.toString() == "/conda/envs/env-${hash}-8a4aa7db8ddb8ce4eb4d450d4814a437" + prefix.toString() == "/conda/envs/env-${hash}-85371202d8820331ff19ae89c0595497" cleanup: folder?.deleteDir()