Version 2.1.0

What's Changed

Full Changelog: 2.0.0...2.1.0

Added

1. Created summary presence/absence tables for NCBI FCS modules #88
2. Added min. system requirements #91
3. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
4. Updated NCBI FCS GX to 0.5.4 #93
5. Updated SYRI to 1.7.0 #104
6. Added a script to automatically check for updates on GitHub/GitLab and post issues
7. Updated modules: UNTAR, MERYL_COUNT, GUNZIP, MINIMAP2_ALIGN, FASTQC

Fixed

1. Fixed a bug where intron_length_distribution was used instead of cds_length_distribution when creating the CDS Length Distribution Graph #95
2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the report.html even when contamination_stops_pipeline was set to false
3. Now NCBI FCS GX module uses all the cores available from the Nextflow task
4. Fixed a bug which caused PLOTSR to fail for certain assembly names #102
5. Now LTRRETRIEVER_LTRRETRIEVER does not crash when the input assembly does not contain any LTRs #92
6. Now LTRRETRIEVER_LTRRETRIEVER does not crash when the input assembly is not writable #98
7. Now soft masked regions are unmasked before computing LAI #117
8. Fixed a bug in ASSEMBLATHON_STATS which caused it to fail on MMC executor due to multiple binds of the bin directory
9. Changed NextFlow to Nextflow
10. Updated citation to Bioinformatics

Dependencies

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

Deprecated

1. Changed default branch name from master to main in nf-core template files
2. Moved version_check.sh to .github/version_checks.sh
3. Moved docs/contributors.sh to .github/contributors.sh
4. Removed dependency on https://github.com/PlantandFoodResearch/nxf-modules.git
5. Replaced nf-core/fastq_trim_fastp_fastqc with nf-core/fastq_fastqc_umitools_fastp which has nf-test unit tests
6. Removed version check on README.md