Tags

Fix bug in binette and others

* Fix remaining conflicts from last realease
* Update documentation
* Fix sample name in taxonomic affiliation plots
* Update multiqc config #210
* Add header to metaWRAP scripts

DSL2 version

- pass to DSL2 to get 2 workflow (Short-read and HiFi)
- gene are named with feature (prot/rrna)
- aln2taxaffi.py refactored to use new_taxdump and prot.accession2taxid.FULL
- add header in diamond output and use it while parsing
- replace mosdepth by samtools coverage
- replace bedtools bamtofastq by samtools fastq
- check gff valididy after prokka
- simplify config files
- update documentation
- chunk assembly to reduce process time of filtering step

- Multiple refactoring actions on metagwgs main script
- Rename some output files and reorganize output directories: i.e: assembly step
- Add mosdepth for contigs depth count + add mosdepth singularity image recipe
- Add taxonomy_dir parameter to use already downloaded taxonomy database
- Add functional tests script to test the pipeline output on reviewed results after functional modifications + add README
- Update documentation for metagwgs
- Change config for test_genotoul_workq parameters
- Change metaspades and megahit to unique assembly process

- Add CI/CD
- Add direct download of Singularity containers
- Add deduplication of reads
- Add filtering of contigs
- Add functional annotation of genes + associated Singularity container
- Add quantification of reads by functional annotation
- Add first strategy of binning (adapted from nf-core/mag v1.0.0)
- Add first strategy of taxonomic affiliation of bins (from nf-core/mag v1.0.0)
- Add summary tables for taxonomic affiliation of contigs
- Add modularity of the pipeline: --step parameter
- Add documentation
- Improvement of MultiQC report: add modules into MultiQC and use of them into metagWGS
- Improve README
- Setting up configuration files
- First optimization of memory and CPU for test data

- Add taxonomic affiliation of contigs
- Add Singularity container
- Setting up configuration files
- First optimization of memory and CPU

First release.