MGnify pipeline maintaince release

There are no functional changes on this release, mostly minor adjustments required for the EMBL-EBI cluster.

What's Changed

• CODON migration changes. by @mberacochea in #40
• A few fixes: by @mberacochea in #43
• Several build_assembly_gff fixes by @mberacochea in #46

Full Changelog: v5.0.6...v5.0.7

MGnify pipeline v5.0 fixes for GFF

• fix GFF file generated by antismash step
• add support of FGS annotations in final GFF
• minor fixes for concatenate step, indexing final fasta file and trimming step

MGnify pipeline v5.0 fixes for cmsearch and seqprep

• added chunking before cmsearch step
• added filtering by reads length before SeqPrep step (only for paired-end samples)

MGnify pipeline v5.0 scripts improvment

• removed step renaming taxonomy files to empty
• improved suppress script
• added flad-file no-tax if taxonomy-summary folder is empty
• added flag-file no-cds if result of functional annotation (FAA) is empty -> do not run further annotation

MGnify pipeline v5.0 simplify conditionals

• removed JSON generation from AntiSmash
• improved Trimmomatic sub-wf
• updated schema.org

MGnify pipeline v5.0 uses CWL conditionals

• conditionals unite before-qc and after-qc steps
• new chunker for DNA sequences
• introduced suppress folder for ITS annotations
• chunking Trimmomatic step for large FastQ files
• conditionals for SeqPrep (use for paired-end reads, skip for single-end reads)
• chunking antismash step
• hmmscan changed to hmmsearch
• all paths for dbs in yml changed from File/Directory types to string

MGnify pipeline v5.0 splited by qc-step

v5.0.1

biom-convert wrapper

stable MGnify pipeline v5.0

5.0.beta

fix return rna-count assembly