LMAS 2.0.0: Update to DSL2

[cimendes]

#LMAS 2.0.0

✨ This PR updates LMAS to Nextflow DSL2. ✨

This is in preparation for the new release. LMAS has been updated to version 2.0.0

Main changes

This PR implements the following changes.

DSL2

The LMAS workflow now enables Nextflow DSL2. The main script has been broken into the following modules:

• preprocessing of the input fastq and fasta sequences
• assembly
• mapping of input fastq to the produces assemblies, and the assemblies to the input fasta reference sequence
• postprocessing for computing all the metrics
• and LMAS report compilation

LMAS script

The main command to run the main script main.nf with nextflow has been wrapped into an LMAS bash script to facilitate usage. Now LMAS can be simply called with

./LMAS <options>

If no options are provided it simply prints out the help message.

Documentation

All documentation has been updated, both in the repository and in readthedocs, to reflect the new changes. Instructions on how to add a new assembler have been updated to nextflow DSL2. Documentation has also been updated to include the ABySS and MetaHipMEr2 assemblers.

Tests

The workflow sanity test has been updated to ensure that the workflow finishes successfully by searching for the final report file.