[Feature] micromambaci

.github/workflows/ci.yml

@@ -52,22 +52,14 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Install mamba
+      - name: Install micromamba
         if: matrix.exec_profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          python-version: 3.9
-          mamba-version: "*"
-          channels: conda-forge,defaults
-
-      # - name: Install micromamba as mamba
-      #   if: matrix.exec_profile == 'conda'
-      #   run: |
-      #     wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
-      #     mv bin/micromamba bin/mamba
-      #     echo "$(pwd)/bin" >> $GITHUB_PATH
-      #     echo "$(pwd)/mamba/bin" >> $GITHUB_PATH
-      #     ./bin/mamba shell init -s bash -p ./mamba
+        run: |
+          wget -qO- https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+          echo "$(pwd)/bin" >> $GITHUB_PATH
+          echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH
+          ./bin/micromamba shell init -s bash -p ./micromamba
+          echo "channels: [conda-forge]\nuse_lockfiles: false" >> ~/.mambarc
 
       - name: Run pipeline with test data
         if: matrix.exec_profile != 'conda'
@@ -82,7 +74,7 @@ jobs:
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,mambaci --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
+          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
       - name: Gather failed logs
         if: failure() || cancelled()
         run: |

nextflow.config

@@ -243,9 +243,9 @@ profiles {
         conda.enabled          = true
         docker.enabled         = false
         singularity.enabled    = false
-        conda.createTimeout = '1 h'
-        conda.useMamba = true
-        process.executor = 'lsf'
+        conda.createTimeout    = '1 h'
+        conda.useMamba         = true
+        process.executor       = 'lsf'
     }
     conda {
         conda.enabled          = true
@@ -256,6 +256,16 @@ profiles {
         charliecloud.enabled   = false
         conda.useMamba    = true
     }
+    micromamba {
+        conda.enabled          = true
+        conda.useMicromamba    = true
+        conda.createTimeout    = '1 h'
+        docker.enabled         = false
+        singularity.enabled    = false
+        podman.enabled         = false
+        shifter.enabled        = false
+        charliecloud.enabled   = false
+    }
     mamba {
         conda.enabled          = true
         conda.useMamba         = true