diff --git a/.github/workflows/test-dragonflye.yml b/.github/workflows/test-dragonflye.yml index c71afde..42d4187 100644 --- a/.github/workflows/test-dragonflye.yml +++ b/.github/workflows/test-dragonflye.yml @@ -26,15 +26,15 @@ jobs: path: bactopia-tests - name: Setup miniconda - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: activate-environment: dragonflye auto-activate-base: false + miniforge-version: latest - name: Setup dragonflye Environment run: | - conda install -y -c conda-forge -c bioconda mamba 'python=3.8.0' - mamba install -y -c conda-forge -c bioconda 'assembly-scan>=0.4.0' any2fasta bwa dnaapler fastp flye 'kmc>=3.1' 'medaka>=1.11.0' miniasm 'nanoq>=0.8.1' perl perl-file-spec perl-findbin 'polypolish>=0.6.0' pilon pigz racon 'rasusa>=1' raven-assembler samtools samclip seqtk porechop + conda install -y -c conda-forge -c bioconda 'assembly-scan>=0.4.0' any2fasta bwa dnaapler fastp flye 'kmc>=3.1' 'medaka>=1.11.0' miniasm 'nanoq>=0.8.1' perl perl-file-spec perl-findbin 'polypolish>=0.6.0' pilon pigz racon 'rasusa>=1' raven-assembler samtools samclip seqtk porechop - name: Environment Information run: uname -a && env