Merge pull request #18 from B-UMMI/dev-dsl2

LMAS 2.0.0: Update to DSL2

.github/workflows/ci_nextflow.yml

@@ -25,4 +25,6 @@ jobs:
           --reference "test/data/tiny_reference.fasta" --max_cpus 2 --max_memory 4.GB \
           --abyss false --bcalm false --gatb_minia false --idba false --metahipmer2 false \
           --minia false --megahit false --metaspades false --spades false --unicycler false \
-          --velvetoptimiser false
+          --velvetoptimiser false
+          FILE=report/index.html 
+          if [ ! -f "$FILE" ]; then echo "Run failed!"; exit 1; else echo "Run successful!"; fi

.gitignore

@@ -160,3 +160,4 @@ 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 $@