Release candidate for 1.4

[GallVp]

1.4 - [04-Mar-2024]

Added

1. Now it is possible to skip FASTP and FASTQC for the HIC module
2. Renamed ASSEMBLY_QC workflow to ASSEMBLYQC
3. Now using nf-core/FASTA_EXPLORE_SEARCH_PLOT_TIDK
4. Now redirecting validation errors to AssemblyQC report
5. Simplified layout of CITATIONS.md file
6. Now using pfr/gff3_validate sub-workflow for gff3 validation
7. Now listing software versions from the versions.yml file
8. Replaced custom GUNZIP module with nf-core/gunzip
9. Replaced custom gt/stat with pfr/gt/stat
10. Replaced custom fasta_validator with nf-core/fastavalidator
11. Added pre-commit version checking
12. Now gt/stat reports extended stats and multiple distribution plots have been added to the report
13. Added a tools tab to the report which lists the tools used by the pipeline to create the report
14. Refactored and cleaned data flows for all the custom sub-workflow
15. Started using nf-core template
16. Started using semantic versioning
17. Moved all python depending packages to 'docker.io/gallvp/python3npkgs:v0.6'

Fixed

1. All modules are now emitting versioning information
2. Fixed a bug which caused LAI to run with null assembly fasta
3. Fixed FASTA_LTRRETRIEVER_LAI sub-workflow so that it respects monoploid_ids parameter.

Dependencies

1. NextFlow!>=23.04.0
2. nf-validation@1.1.3

Deprecated

1. Removed BIOCODE GFF3 STATS owing to its frequent failures

[GallVp]

Fixes and Closes #78, #73, #62, #58

Deprecates and Closes #53, #67 as EDTA is removed from the pipeline