mag 5.5.0 - Purple Penguin

Added

• #908 - Add nf-test snapshot for test_single_end profile (by @dialvarezs)
• #1028 - Add nf-test snapshot for test_longread_alternatives profile (by @dialvarezs)
• #1029 - Add nf-test snapshot for test_hybrid profile (by @dialvarezs)
• #1037 - Complement usage documentation with guidance on pipeline defaults, choices and alternatives (by @d4straub and @jfy133 )
• #1039 - Add nf-test snapshot for test_longread profile (started by @brovolia, finished by @dialvarezs)
• #1041 - Refined and corrected unclear section of metromap (by @jfy133)
• #1042 - Add nf-test snapshot for test_default profile (by @dialvarezs)
• #1044 - Add new --gtdbtk_place_species parameter (by @dialvarezs)
• #1047 - Add --gtdbtk_single_job to run GTDB-Tk classification for all bins in a single job (requested by @sarah-shah-bioinf, by @dialvarezs)
• #1048 - Add optional PyPOLCA polishing for long-read assemblies via --run_pypolca (by @Harshita-sriv)
• #1055 - Add dedicated page describing resource usage (by @jfy133)
• #1057 - Add skip_fastqc switch (by @jorondo1)
• #1059 - Add --filtlong_filtering_by_shortreads parameter to enable filtlong's short-read-based long read filtering (by @dialvarezs)
• #1062 - Add --bin_seqkit_stats_max_forks parameter to cap concurrent bin-stats jobs (by @dialvarezs)
• #1063 - Add new --ale_per_base_output parameter to enable ALE per-base output (by @dialvarezs)

Changed

• #1011 - Reverted CheckM2 database download workaround from #966 (by @dialvarezs)
• #1020 - Update CONCOCT subworkflow and modules (by @dialvarezs)
• #1030 - Updated to nf-core 4.0.2 template (by @dialvarezs)
• #1044 - Updated GTDB-Tk to v2.7.2 / GTDB r232 (by @dialvarezs)
• #1059 - Changed the default long read filtering tool from filtlong to chopper (by @dialvarezs)
• #1060 - Updated module tags to make them more specific (by @dialvarezs)
• #1061, #1064 - Speed up binning by not waiting for all mapping jobs to finish before starting (by @dialvarezs)
• #1062 - Remove grouping to prevent bin QC blocking by waiting for all binners (by @dialvarezs)
• #1063 - Run ALE with --metagenome and disable its per-base output by default (by @dialvarezs)
• #1065 - Improved efficiency by removing usage of per-bin GUNZIP module for bins and unbinned contigs and allowing gzip support for all modules (by @dialvarezs)
• #1066 - Improved efficiency by removing channel "locks" on Seqkit, QUAST, and GTDB-Tk (by @dialvarezs)
• #1070 - Update BUSCO nf-core module (by @dialvarezs)
• #1071 - Improved efficiency by batching DASTOOL_FASTATOCONTIG2BIN per binner instead of per bin (by @dialvarezs)
• #1074 - Exclude BUSCO output directories to reduce storage usage in output dir (by @dialvarezs)
• #1075 - Update output documentation to reflect BUSCO complete directory no longer being published (by @dialvarezs)
• #1079 - Add exit code 247 to the MEGAHIT retry error strategy (by @dialvarezs)
• #1080 - Updated to nf-core 4.0.3 TEMPLATE (by @dialvarezs)
• #1081 - Use subset database for geNomad (by @dialvarezs)
• #1084 - Disable NanoPlot static plot image files by default, since it depends on Chrome installed (by @dialvarezs)
• #1088 - Update Prokka (to v1.15.6), Prodigal and PyDamage modules, fixing conda/container output mismatches (by @dialvarezs)
• #1088 - Run GTDB-Tk with a single CPU on the test_single_end profile, so its outputs no longer depend on the machine running the test (by @dialvarezs)
• #1091 - Optimize process resource configs (by @dialvarezs)

Fixed

• #1011 - Fix issue making CheckM2 running only for one sample per run (by @dialvarezs)
• #1012 - Prevent adapter trimming with Porechop on PacBio reads (by @dialvarezs)
• #1016 - Merge input reads on assembly input to prevent repeated filenames on multi-run samples (reported by @erikrikarddaniel, fix by @dialvarezs)
• #1017 - Prevent ALE running on long read assemblies when a sample has both LR and SR data (reported by @jfy133, fix by @dialvarezs)
• #1018 - Ignore catpack/summarise errors, since it's a limitation from the tool (reported by @jfy133, fix by @dialvarezs)
• #1018 - Feed catpack/contig with merged unbinned output to prevent execution errors (reported by @Juassis, fix by @dialvarezs)
• #1021 - Prevent execution of gtdbtk/summary when no bins pass QC (reported by @jfy133, fix by @dialvarezs)
• #1031 - Fix hybrid co-assembly with SPAdes (short & long reads with --coassemble_group) (fix by @d4straub)
• #1049 - Fix publishing issue with gtdbtk/classifywf (by @dialvarezs)
• #1058 - Make create_metabinner_bins.py save gzipped bin files to prevent NFS race condition (by @dialvarezs)
• #1069 - Exclude eukaryotic bins from CheckM2, which only supports bacterial and archaeal genomes (by @dialvarezs)
• #1076 - Add missing PyPOLCA citations to README, CITATIONS.md and the pipeline citation/bibliography text (by @dialvarezs)
• #1078 - Sort bins before GTDB-Tk classification so order-sensitive outputs are reproducible across environments (by @dialvarezs)
• #1084 - Update Prokka nf-core module, which pins GNU parallel to fix Prokka failures with Conda (by @dialvarezs)
• #1086 - Rename MaxBin2 bins inside the MAXBIN2 module via a patch instead of the ADJUST_MAXBIN2_EXT local module, which emitted dangling symlinks rather than bin contents on remote filesystems (by @dialvarezs)
• #1086 - Copy instead of move staged bins in TIARA_CLASSIFY, which emitted dangling symlinks rather than bin contents on remote filesystems (by @dialvarezs)
• #1086 - Match bin filenames exactly in TIARA_CLASSIFY so that e.g. bin .1 no longer also picks up bin .10 (by @dialvarezs)
• #1087 - Use non-mutating toSorted instead of in-place sort on shared channel items, which could cause ConcurrentModificationException failures (by @dialvarezs)
• #1093 - Ignore CheckM storage/ subdirectories in nf-test snapshots, whose contents vary between runs and machines (by @dialvarezs)
• #1094 - Convert depths in a single streaming pass, so CONVERT_DEPTHS no longer writes a decompressed copy of the depth file to the work directory and re-reads it once per read set, which stalled short-read assemblies for hours on object-backed work directories (by @dialvarezs)

Dependencies

Tool	Previous version	New version
BUSCO	6.0.0	6.1.0
GTDB (database)	r226	r232
GTDB-Tk	2.5.2	2.7.2
MultiQC	1.31	1.34
Nextflow	25.10.4	26.04.0
nf-core	3.5.1	4.0.3
nf-schema	2.5.1	2.7.2
Prokka	1.14.6	1.15.6
pypolca		0.4.0

Deprecated

• #908 - Removed local quast_bins_summary in favor of csvtk/concat (by @dialvarezs)
• #1018 - Remove mag_depths_plot local module (by @dialvarezs)
• #1018 - Deprecated --gtdbtk_skip_aniscreen in favor of --gtdbtk_place_species (by @dialvarezs)
• #1067 - Deprecated --skip_metaeuk as it has no effect, MetaEuk is gated by --metaeuk_db / --metaeuk_mmseqs_db (by @dialvarezs)
• #1086 - Removed adjust_maxbin2_ext local module, replaced by a patch on the MAXBIN2 nf-core module (by @dialvarezs)

Full Changelog: 5.4.2...5.5.0