update dev with main

.github/workflows/ci_nextflow.yml

@@ -0,0 +1,57 @@
+name: CI - Nextflow test
+# This workflow is triggered on pushes and PRs to the repository.
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_ver: ['21.04.1', '']
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - name: Install Nextflow
+        run: |
+          export NXF_VER=${{ matrix.nxf_ver }}
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Basic workflow tests
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile docker --fastq "test/data/tiny_{1,2}.*" \
+          --reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
+          --abyss false --gatb_minia false --idba false --metahipmer2 false \
+          --minia false --megahit false --metaspades false --spades false --unicycler false \
+          --velvetoptimiser false
+          FILE=report/index.html 
+          if [ ! -f "$FILE" ]; then echo "Run failed!"; exit 1; else echo "Run successful!"; fi
+
+  singularity:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        singularity_version: ['3.6.4']
+        nxf_ver: ['21.04.1', '']
+    steps:
+      - uses: actions/checkout@v1
+      - uses: eWaterCycle/setup-singularity@v6
+        with:
+          singularity-version: ${{ matrix.singularity_version }}
+      - name: Install Nextflow
+        run: |
+          export NXF_VER=${{ matrix.nxf_ver }}
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+      - name: Basic workflow tests
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile singularity --fastq "test/data/tiny_{1,2}.*" \
+          --reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
+          --abyss false --gatb_minia false --idba false --metahipmer2 false \
+          --minia false --megahit false --metaspades false --spades false --unicycler false \
+          --velvetoptimiser false
+          FILE=report/index.html 
+          if [ ! -f "$FILE" ]; then echo "Run failed!"; exit 1; else echo "Run successful!"; fi

.github/workflows/ci_templates.yml

@@ -0,0 +1,29 @@
+name: CI - Python templates test
+
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+         python-version: 3.8
+
+      - name: install dependencies
+        run: |
+         python -m pip install --upgrade pip
+         pip install -r docker/LMAS/requirements.txt
+         pip install pytest
+
+      - name: run pytest
+        run: pytest
+

.gitignore

@@ -158,3 +158,6 @@ test/misassembly_test.json
 test/misassembly_test_all.json
 docs/resources/.DS_Store
 .DS_Store
+results/
+report/
+!modules/

LMAS

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+# This is a wrapper around LMAS-nf. 
+# By default `LMAS` will attempt to execute the main Nextflow pipeline.
+# If no user input is provided, it prints the help message
+
+# If no user input, print usage
+if [[ $# == 0 ]]; then
+    nextflow run main.nf --help
+    exit
+fi
+
+# Run the pipeline
+nextflow run main.nf $@