Merge pull request #61 from TRON-Bioinformatics/56_add_mamba_support

Add mamba support and update pangolin lineage determination

.github/workflows/automated_tests.yml

@@ -14,6 +14,7 @@ jobs:
         java-version: '11'
     - uses: conda-incubator/setup-miniconda@v2
       with:
+        mamba-version: "*"
         auto-update-conda: true
         channels: conda-forge,bioconda,defaults
     - name: Install dependencies
@@ -30,4 +31,4 @@ jobs:
     - name: Run tests
       run: |
         export NXF_VER=22.04.5
-        make
+        make

.gitlab-ci.yml

@@ -8,11 +8,23 @@ before_script:
   #- pip3 install biopython==1.76
   - wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow
   - nextflow help
-  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
   - mkdir /root/.conda
-  - bash Miniconda3-latest-Linux-x86_64.sh -b && cp /root/miniconda3/bin/* /usr/local/bin/
-  - rm -f Miniconda3-latest-Linux-x86_64.sh
-  - conda --version
+  - bash Mambaforge-Linux-x86_64.sh -b -p /usr/local/bin/conda
+  - rm -f Mambaforge-Linux-x86_64.sh
+  - source /usr/local/bin/conda/etc/profile.d/conda.sh
+  - source /usr/local/bin/conda/etc/profile.d/mamba.sh
+  - which mamba 
+  - mamba --version
+  # this is a workaround for https://github.com/mamba-org/mamba/issues/1993
+  - echo "use_lockfiles:" >> ~/.mambarc
+  - echo "  - false" >> ~/.mambarc
+  - echo "channels:" >> ~/.mambarc
+  - echo "  - defaults" >> ~/.mambarc
+  - echo "  - conda-forge" >> ~/.mambarc
+  - echo "  - bioconda" >> ~/.mambarc
+  - cat ~/.mambarc
+
 
 stages:
   - test

modules/07_lineage_annotation.nf

@@ -9,7 +9,7 @@ process PANGOLIN_LINEAGE {
     publishDir "${params.output}", mode: "copy"
     tag "${name}"
 
-    conda (params.enable_conda ? "bioconda::pangolin=4.1.2" : null)
+    conda (params.enable_conda ? "bioconda::pangolin=4.3" : null)
 
     input:
         tuple val(name), val(caller), file(fasta)

nextflow.config

@@ -32,6 +32,7 @@ profiles {
   conda {
     params.enable_conda = true
     conda.enabled = true
+    conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {