Skip to content

Latest commit

 

History

History
266 lines (188 loc) · 18.2 KB

CHANGELOG.md

File metadata and controls

266 lines (188 loc) · 18.2 KB
Raw

nf-core/mag: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v2.3.0 - [2023/03/02]

Added

  • #350 - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133 and @skrakau)
  • #353 - Added the busco_clean parameter to optionally clean each BUSCO directory after a successful (by @prototaxites)
  • #361 - Added the skip_clipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skip_clipping, keep_phix and without specifying a host genome or fasta file skips the FASTQC_TRIMMED process (by @prototaxites)
  • #365 - Added CONCOCT as an additional (optional) binning tool (by @jfy133)
  • #366 - Added CAT_SUMMARISE process and cat_official_taxonomy parameter (by @prototaxites)
  • #372 - Allow CAT_DB to take an extracted database as well as a tar.gz file (by @prototaxites).
  • #380 - Added support for saving processed reads (clipped, host removed etc.) to results directory (by @jfy133)
  • #394 - Added GUNC for additional chimeric bin/contamination QC (added by @jfy133)

Changed

  • #340,#368,#373 - Update to nf-core 2.7.2 TEMPLATE (by @jfy133, @d4straub, @skrakau)
  • #373 - Removed parameter --enable_conda. Updated local modules to new conda syntax and updated nf-core modules (by @skrakau)
  • #385 - CAT also now runs on unbinned contigs as well as binned contigs (added by @jfy133)
  • #399 - Removed undocumented BUSCO_PLOT process (previously generated *.busco_figure.png plots unsuitable for metagenomics) (by @skrakau).

Fixed

  • #345 - Bowtie2 mode changed to global alignment for ancient DNA mode (--very-sensitive mode) to prevent soft clipping at the end of reads when running in local mode. (by @maxibor)
  • #349 - Add a warning that pipeline will reset minimum contig size to 1500 specifically MetaBAT2 process, if a user supplies below this threshold. (by @jfy133)
  • #352 - Escape the case in the BUSCO module that BUSCO can just detect a root lineage but is not able to find any marker genes (by @alexhbnr)
  • #355 - Include error code 21 for retrying with higher memory for SPAdes and hybridSPAdes (by @mglubber)

Dependencies

Tool Previous version New version
BUSCO 5.1.0 5.4.3
BCFtools 1.14 1.16
Freebayes 1.3.5 1.3.6
SAMtools 1.15 1.16.1

v2.2.1 - 2022/08/25

Added

Changed

Fixed

  • #328 - Fix too many symbolic links issue in local convert_depths module (reported by @ChristophKnapp and fixed by @apeltzer, @jfy133)
  • #329 - Each sample now gets it's own result directory for PyDamage analysis and filter (reported and fixed by @maxibor)

Dependencies

v2.2.0 - 2022/06/14

Added

  • #263 - Restructure binning subworkflow in preparation for aDNA workflow and extended binning
  • #247 - Add ancient DNA subworkflow
  • #263 - Add MaxBin2 as second contig binning tool
  • #285 - Add AdapterRemoval2 as an alternative read trimmer
  • #291 - Add DAS Tool for bin refinement
  • #319 - Activate pipeline-specific institutional nf-core/configs

Changed

  • #269,#283,#289,#302 - Update to nf-core 2.4 TEMPLATE
  • #286 - Cite our publication instead of the preprint
  • #291, #299 - Add extra results folder GenomeBinning/depths/contigs for [assembler]-[sample/group]-depth.txt.gz, and GenomeBinning/depths/bins for bin_depths_summary.tsv and [assembler]-[binner]-[sample/group]-binDepths.heatmap.png
  • #315 - Replace base container for standard shell tools to fix problems with running on Google Cloud

Fixed

  • #290 - Fix caching of binning input
  • #305 - Add missing Bowtie2 version for process BOWTIE2_PHIX_REMOVAL_ALIGN to software_versions.yml
  • #307 - Fix retrieval of GTDB-Tk version (note about newer version caused error in CUSTOM_DUMPSOFTWAREVERSIONS)
  • #309 - Fix publishing of BUSCO busco_downloads/ folder, i.e. publish only when --save_busco_reference is specified
  • #321 - Fix parameter processing in BOWTIE2_REMOVAL_ALIGN (which was erroneously for BOWTIE2_PHIX_REMOVAL_ALIGN)

Dependencies

Tool Previous version New version
fastp 0.20.1 0.23.2
MultiQC 1.11 1.12

v2.1.1 - 2021/11/25

Added

  • #240 - Add prodigal to predict protein-coding genes for assemblies.
  • #241 - Add parameter --skip_prodigal.
  • #244 - Add pipeline preprint information.
  • #245 - Add Prokka to annotate binned genomes.

Changed

  • #249 - Update workflow overview figure.
  • #258 - Updated MultiQC 1.9 to 1.11.
  • #260 - Updated SPAdes 3.13.1 -> 3.15.3, MEGAHIT 1.2.7 -> 1.2.7

Fixed

  • #256 - Fix --skip_busco.
  • #236 - Fix large assemblies (> 4 billion nucleotides in length).
  • #254 - Fix MetaBAT2 error with nextflow version 21.10.x (21.04.03 is the latest functional version for nf-core/mag 2.1.0).
  • #255 - Update gtdbtk conda channel.
  • #258 - FastP results are now in MultiQC.

v2.1.0 - 2021/07/29

Added

  • #212, #214 - Add bin abundance estimation based on median sequencing depths of corresponding contigs (results are written to results/GenomeBinning/bin_depths_summary.tsv and results/GenomeBinning/bin_summary.tsv) #197.
  • #214 - Add generation of (clustered) heat maps with bin abundances across samples (using centered log-ratios)
  • #217 - Publish genes predicted with Prodigal within BUSCO run (written to results/GenomeBinning/QC/BUSCO/[assembler]-[bin]_prodigal.gff).

Changed

  • #218 - Update to nf-core 2.0.1 TEMPLATE (DSL2)

Fixed

  • #226 - Fix handling of BUSCO output when run in auto lineage selection mode and selected specific lineage is the same as the generic one.

v2.0.0 - 2021/06/01

Added

  • #179 - Add BUSCO automated lineage selection functionality (new default). The pameter --busco_auto_lineage_prok can be used to only consider prokaryotes and the parameter --busco_download_path to run BUSCO in offline mode.
  • #178 - Add taxonomic bin classification with GTDB-Tk v1.5.0 (for bins filtered based on BUSCO QC metrics).
  • #196 - Add process for CAT database creation as an alternative to using pre-built databases.

Changed

  • #162 - Switch to DSL2
  • #162 - Changed --input file format from TSV to CSV format, requires header now
  • #162 - Update README.md, docs/usage.md and docs/output.md
  • #162 - Update FastP from version 0.20.0 to 0.20.1
  • #162 - Update Bowtie2 from version 2.3.5 to 2.4.2
  • #162 - Update FastQC from version 0.11.8 to 0.11.9
  • #172 - Compressed discarded MetaBAT2 output files
  • #176 - Update CAT DB link
  • #179 - Update BUSCO from version 4.1.4 to 5.1.0
  • #179 - By default BUSCO now performs automated lineage selection instead of using the bacteria_odb10 lineage as reference. Specific lineage datasets can still be provided via --busco_reference.
  • #178 - Change output file: results/GenomeBinning/QC/quast_and_busco_summary.tsv -> results/GenomeBinning/bin_summary.tsv, contains GTDB-Tk results as well.
  • #191 - Update to nf-core 1.14 TEMPLATE
  • #193 - Compress CAT output files #180
  • #198 - Requires nextflow version >= 21.04.0
  • #200 - Small changes in GitHub Actions tests
  • #203 - Renamed fastp params and improved description in documentation: --mean_quality -> --fastp_qualified_quality, --trimming_quality -> --fastp_cut_mean_quality

Fixed

  • #175 - Fix bug in retrieving the --max_unbinned_contigs longest unbinned sequences that are longer than --min_length_unbinned_contigs (split_fasta.py)
  • #175 - Improved runtime of split_fasta.py in METABAT2 process (important for large assemblies, e.g. when computing co-assemblies)
  • #194 - Allow different folder structures for Kraken2 databases containing *.k2d files #187
  • #195 - Fix documentation regarding required compression of input FastQ files #160
  • #196 - Add process for CAT database creation as solution for problem caused by incompatible DIAMOND version used for pre-built CAT database and CAT classification #90, #188

v1.2.0 - 2021/02/10

Added

  • #146 - Add --coassemble_group parameter to allow group-wise co-assembly
  • #146 - Add --binning_map_mode parameter allowing different mapping strategies to compute co-abundances used for binning (all, group, own)
  • #149 - Add two new parameters to allow custom SPAdes and MEGAHIT options (--spades_options and --megahit_options)

Changed

  • #141 - Update to nf-core 1.12.1 TEMPLATE
  • #143 - Manifest file has to be handed over via --input parameter now
  • #143 - Changed format of manifest input file: requires a '.tsv' suffix and additionally contains group ID
  • #143 - TSV --input file allows now also entries containing only short reads
  • #145 - When using TSV input files, uses sample IDs now for FastQC instead of basenames of original read files. Allows non-unique file basenames.

Removed

  • #143 - Change parameter: --manifest -> --input

v1.1.2 - 2020/11/24

Changed

  • #135 - Update to nf-core 1.12 TEMPLATE

Fixed

  • #133 - Fixed processing of --input parameter #131

v1.1.1 - 2020/11/10

Added

  • #121 - Add full-size test
  • #124 - Add worfklow overview figure to README

Changed

  • #123 - Update to new nf-core 1.11 TEMPLATE

Fixed

  • #118 - Fix seaborn to v0.10.1 to avoid nanoplot error
  • #120 - Fix link to CAT database in help message
  • #124 - Fix description of CAT process in output.md

v1.1.0 - 2020/10/06

Added

  • #35 - Add social preview image
  • #49 - Add host read removal with Bowtie 2 and according custom section to MultiQC
  • #49 - Add separate MultiQC section for FastQC after preprocessing
  • #65 - Add MetaBAT2 RNG seed parameter --metabat_rng_seed and set the default to 1 which ensures reproducible binning results
  • #65 - Add parameters --megahit_fix_cpu_1, --spades_fix_cpus and --spadeshybrid_fix_cpus to ensure reproducible results from assembly tools
  • #66 - Export depth.txt.gz into result folder
  • #67 - Compress assembly files
  • #82 - Add nextflow_schema.json
  • #104 - Add parameter --save_busco_reference

Changed

  • #56 - Update MetaBAT2 from v2.13 to v2.15
  • #46 - Update MultiQC from v1.7 to v1.9
  • #88 - Update to new nf-core 1.10.2 TEMPLATE
  • #88 - --reads is now removed, use --input instead
  • #101 - Prevented PhiX alignments from being stored in work directory #97
  • #104, #111 - Update BUSCO from v3.0.2 to v4.1.4

Fixed

  • #29 - Fix MetaBAT2 binning discards unbinned contigs #27
  • #31, #36, #76, #107 - Fix links in README
  • #47 - Fix missing MultiQC when --skip_quast or --skip_busco was specified
  • #49, #89 - Added missing parameters to summary
  • #50 - Fix missing channels when --keep_phix is specified
  • #54 - Updated links to minikraken db
  • #54 - Fixed Kraken2 dp preparation: allow different names for compressed archive file and contained folder as for some minikraken dbs
  • #55 - Fixed channel joining for multiple samples causing MetaBAT2 error #32
  • #57 - Fix number of threads used by MetaBAT2 program jgi_summarize_bam_contig_depths
  • #70 - Fix SPAdes memory conversion issue #61
  • #71 - No more ignoring errors in SPAdes assembly
  • #72 - No more ignoring of BUSCO errors
  • #73, #75 - Improved output documentation
  • #96 - Fix missing bin names in MultiQC BUSCO section #78
  • #104 - Fix BUSCO errors causing missing summary output #77

Deprecated

  • #29 - Change depreciated parameters: --singleEnd -> --single_end, --igenomesIgnore -> --igenomes_ignore

v1.0.0 - 2019/12/20

Initial release of nf-core/mag, created with the nf-core template.

Added

  • short and long reads QC (fastp, porechop, filtlong, fastqc)
  • Lambda and PhiX detection and filtering (bowtie2, nanolyse)
  • Taxonomic classification of reads (centrifuge, kraken2)
  • Short read and hybrid assembly (megahit, metaspades)
  • metagenome binning (metabat2)
  • QC of bins (busco, quast)
  • annotation (cat/bat)