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mag 2.4.0 - Grey Hammerhead
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@jfy133 jfy133 released this 26 Sep 09:01
· 544 commits to master since this release
2.4.0
18a1645
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Learn about vigilant mode.

Added

  • #497 - Adds support for pointing at a local db for krona, using the parameter --krona_db (by @willros).
  • #395 - Adds support for fast domain-level classification of bins using Tiara, to allow bins to be separated into eukaryotic and prokaryotic-specific processes.
  • #422 - Adds support for normalization of read depth with BBNorm (added by @erikrikarddaniel and @fabianegli)
  • #439 - Adds ability to enter the pipeline at the binning stage by providing a CSV of pre-computed assemblies (by @prototaxites)
  • #459 - Adds ability to skip damage correction step in the ancient DNA workflow and just run pyDamage (by @jfy133)
  • #364 - Adds geNomad nf-core modules for identifying viruses in assemblies (by @PhilPalmer and @CarsonJM)
  • #481 - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
  • #437 - --gtdb_db also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
  • #494 - Adds support for saving the BAM files from Bowtie2 mapping of input reads back to assembly (fix by @jfy133)

Changed

  • #428 #467 - Update to nf-core 2.8, 2.9 TEMPLATE (by @jfy133)
  • #429 - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
  • #441 - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
  • #442 - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
  • #444 - Moved BUSCO bash code to script (by @jfy133)
  • #477 - --gtdb parameter is split into --skip_gtdbtk and --gtdb_db to allow finer control over GTDB database retrieval (fix by @jfy133)
  • #500 - Temporarily disabled downstream processing of both refined and raw bins due to bug (by @jfy133)

Fixed

  • #496 - Fix help text for paramters --bowtie2_mode, spades_options and megahit_options (by @willros)
  • #400 - Fix duplicated Zenodo badge in README (by @jfy133)
  • #406 - Fix CheckM database always downloading, regardless if CheckM is selected (by @jfy133)
  • #419 - Fix bug with busco_clean parameter, where it is always activated (by @prototaxites)
  • #426 - Fixed typo in help text for parameters --host_genome and --host_fasta (by @tillenglert)
  • #434 - Fix location of samplesheet for AWS full tests (reported by @Lfulcrum, fix by @jfy133)
  • #438 - Fixed version inconsistency between conda and containers for GTDBTK_CLASSIFYWF (by @jfy133)
  • #439 - Fix bug in assembly input (by @prototaxites)
  • #447 - Remove default: None from parameter schema (by @drpatelh)
  • #449 - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133)
  • #470 - Fix binning preparation from running even when binning was requested to be skipped (reported by @prototaxites, fix by @jfy133)
  • #480 - Improved -resume reliability through better meta map preservation (reported by @prototaxites, fix by @jfy133)
  • #493 - Update METABAT2 nf-core module so that it reduced the number of unnecessary file moves, enabling virtual filesystems (fix by @adamrtalbot)
  • #500 - Fix MaxBin2 bins not being saved in results directly properly (reported by @Perugolate, fix by @jfy133)

Dependencies

Tool Previous version New version
BCFtools 1.16 1.17
SAMtools 1.16.1 1.17
fastp 0.23.2 0.23.4
MultiQC 1.14 1.15

Contributors

alneberg, erikrikarddaniel, and 13 other contributors
Assets 2
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