nf-core/mag: mag 5.3.0 - Rainbow Rattlesnake

Added #905 - Add nf-test snapshot for test_assembly_input profile (by @dialvarezs) #930 - Add binner SemiBin2 (by @d4straub) #861 - Added --generate_bigmag_file to execute the bigmag workflow that generates the file to be used as input for BIgMAG (added by @jeffe107) Changed #932 - Replaced usages of deprecated Channel() with channel() and fix other LSP warnings (by @dialvarezs) #937 - Updated to nf-core 3.5.1 TEMPLATE (by @dialvarezs) #938 - Update nf-core modules (by @dialvarezs) Fixed #894 - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs) #927 - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub) #929 - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites) #943 - Fixed concatenation of BUSCO summaries with uneven columns by changing from csvtk to qsv (reported by @jfy133 and @julianu, fix by @dialvarezs) #943 - Fixed creation of the Tiara report channel used for concatenation (by @dialvarezs) #945 - Skip mixing of GTDB-Tk MultiQC files when binning is skipped (reported by @amizeranschi, fix by @dialvarezs) #953 - metaSPAdes retries upon error 250 (out of memory), rather than finishing the pipeline. #954 - Skip GTDB-Tk when no bin QC tool is enabled and add warning messages (fix by @dialvarezs) #956 - Support long reads assemblers in assembly input (fix by @dialvarezs) Dependencies | Tool | Previous version | New version | | -------- | ---------------- | ----------- | | bcftools | 1.21 | 1.22 | | csvtk | 0.31.0 | | | fastp | 0.24.0 | 1.0.1 | | geNomad | 1.11.1 | 1.11.2 | | metamdbg | 1.1 | 1.2 | | mmseqs | 17.b804f | 18.8cc5c | | nf-core | | 3.5.1 | | qsv | | 5.1.0 | | samtools | 1.21 | 1.22.1 | | SemiBin2 | | 2.2.0 | Deprecated #943 - Remove csvtk/concat module (by @dialvarezs).