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nf-core/mag: Changelog

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

v1.2.0 - 2020/02/10

`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.

`Deprecated`

#143 - Change depreciated parameters: --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)