Remove defaults channel (#85)

* Remove `defaults` channel

* Bump version

* Update test workflow

Author: dfornika

.github/workflows/pull_request.yml

@@ -1,16 +1,30 @@
 on:
+  pull_request:
+    branches:
+      - main
   push:
     branches:
-    - main
+      - main
+  workflow_dispatch:
 name: Tests
 jobs:
   test:
+    strategy:
+      fail-fast: false
+      matrix:
+        nextflow_version: ["21.04.3", "23.10.1"]
     name: Run tests
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@master
+    - uses: actions/checkout@v4
     - name: create artifacts dir to save test logs
       run: mkdir artifacts
+    - name: Setup Java
+      uses: actions/setup-java@v4
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+        architecture: x64
     - name: Cache Miniconda Installation
       id: cache-miniconda
       uses: pat-s/[email protected]
@@ -80,6 +94,8 @@ jobs:
       run: bash .github/scripts/install_conda.sh
     - name: Install Nextflow
       if: steps.cache-nextflow.outputs.cache-hit != 'true'
+      env:
+        NXF_VER: ${{ matrix.nextflow_version }}
       run: bash .github/scripts/install_nextflow.sh
     - name: Install ncbi-acc-download
       if: steps.cache-miniconda.outputs.cache-hit != 'true'

.github/workflows/push_main.yml renamed to .github/workflows/tests.yml

@@ -1,8 +1,7 @@
-name: routine-qc
+name: routine-sequence-qc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python=3
   - fastqc=0.11.9

environments/environment.yml

@@ -3,7 +3,7 @@ manifest {
   description = 'Routine Sequence QC'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '0.4.4'
+  version = '0.4.5'
 }
 
 params {