Releases | Open Source Science

`Added`

#730 - Added --busco_db_lineage to allow specifying a specific lineage for BUSCO database (added by @jfy133, @dialvarezs)
#730 - Added a new documentation section on database setup (by @jfy133, @dialvarezs)
#784 - Added --bin_min_size and --bin_max_size parameters to filter out bins based on size (requested by @maxibor, @alexhbnr, added by @jfy133, @prototaxites)
#793 - Document use of a SquashFS image with --gtdb_db, useful for limited inode infrastructure (by @muniheart)
#805 - Add support for fastp's --trim_poly_g option (by @jfy133)

`Changed`

#730 - Migrate from local BUSCO module to nf-core one, updating version (by @dialvarezs)
#730 - Use BUSCO database from nf-core test datasets (by @dialvarezs)
#788 - Tweak method of loading GTDB database in GTDBTK_CLASSIFYWF for more stability (reported by @alexhbnr, fix by @jfy133)
#800 - Default branch is now set to main (by @jfy133 and @mirpedrol)
#801 - Increase CheckM memory requests to match recommended requirements (by @jfy133)

`Fixed`

#789 - Improve --bowtie2_mode description to clarify default settings (reported by @IceGreb, fix by @jfy133)
#798 - Fix overly strict database validation for --metauk_db and improve documentation (reported by @ruqse, fix by @jfy133)
#804 - Fix broken memory specification for FASTQC (reported by @jmichaelegana, fix by @awgymer & @jfy133)

`Dependencies`

| Tool | Previous version | New version | | -------- | ---------------- | ----------- | | BUSCO | 5.4.3 | 5.8.3 | | csvtk | | 0.31.0 | | nextflow | 24.04.2 | 25.04.2 |

`Deprecated`

#730 - Remove --busco_auto_lineage_prok due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)

- Nextflow
Published by jfy133 9 months ago

`Added`

#745 - Added pipeline parameter spades_downstreaminput to use contigs instead of scaffolds (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
#745 - Added trimmomatic as an additional pre-processing tool (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
#745 - Added parameters for concoct/cut_up_fasta.py including bin_concoct_chunksize, bin_concoct_overlap and bin_concoct_donotconcatlast (by @Pranjal-Bioinfo, @jfy133, @GallVp & @sateeshperi).
#777 - Improved input validation through additional JSON keywords and error messages (by @agusinac)

`Changed`

#774 - Update CheckM2 to v1.1.0 and default database (by @dialvarezs).

`Fixed`

#726 - Fix formatting errors to follow Nextflow best practice (by @dialvarezs).
#769 - Fix megahit not emitting correct filenames due to suboptimal arguments ordering (reported and fix by @IceGreb)
#771 - Fix misspecified checkm2 database parameter check (reported by @dpelegri and fix by @jfy133)

`Dependencies`

| Tool | Previous version | New version | | ------- | ---------------- | ----------- | | CheckM2 | 1.0.2 | 1.1.0 | | SPAdes | 4.0.0 | 4.1.0 |

- Nextflow
Published by jfy133 11 months ago

mag - mag 3.3.1 - [2025-02-13]

`Added`

#758 - Added new diagram in metro-map style (by @jfy133, @prototaxites, @d4straub)

`Changed`

#731 - Updated to nf-core 3.1.2 TEMPLATE (by @jfy133)
#755 - Updated to nf-core 3.2.0 TEMPLATE (by @jfy133)

`Fixed`

#748 - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor)
#752 - Fix QUAST results not being displayed when skipping certain steps (reported by @amizeranschi, fix by @jfy133)
#753 - Fix iGenomes reference support for host removal reference genome (reported by @Thomieh73, fix by @jfy133)
#759 - Fixed parameters that allow both files or directories to not error with directories, and general file input validation improvements (reported by @mjfi2sb3, fix by @jfy133)

- Nextflow
Published by jfy133 about 1 year ago

mag - mag 3.3.0 - Red Reindeer

`Added`

#692 - Added Nanoq as optional longread filtering tool (added by @muabnezor)
#692 - Added chopper as optional longread filtering tool and/or phage lambda removal tool (added by @muabnezor)
#707 - Make Bin QC a subworkflow (added by @dialvarezs)
#707 - Added CheckM2 as an alternative bin completeness and QC tool (added by @dialvarezs)
#708 - Added --exclude_unbins_from_postbinning parameter to exclude unbinned contigs from post-binning processes, speeding up Prokka in some cases (added by @dialvarezs)
#732 - Added support for Prokka's compliance mode with --prokka_with_compliance --prokka_compliance_centre <xyz> (reported by @audy and @Thomieh73, added by @jfy133)

`Changed`

#731 - Updated to nf-core 3.1.0 TEMPLATE (by @jfy133)

`Fixed`

#707 - Fixed channel passed as GUNC input (added by @dialvarezs)
#724 - Fix quoting in utils_nfcore_mag_pipeline/main.nf (added by @dialvarezs)
#716 - Make short read processing a subworkflow (added by @muabnezor)
#708 - Fixed channel passed as GUNC input (added by @dialvarezs)
#729 - Fixed misspecified multi-FASTQ input for single-end data in MEGAHIT (reported by John Richards, fix by @jfy133)

`Dependencies`

| Tool | Previous version | New version | | ------- | ---------------- | ----------- | | CheckM | 1.2.1 | 1.2.3 | | CheckM2 | | 1.0.2 | | chopper | | 0.9.0 | | GUNC | 1.0.5 | 1.0.6 | | nanoq | | 0.10.0 |

- Nextflow
Published by jfy133 about 1 year ago

mag - mag 3.2.1 [2024-10-30]

`Fixed`

#707 - Fix missing space resulting in malformed args for MEGAHIT (reported by @d4straub, fix by @jfy133)

- Nextflow
Published by jfy133 over 1 year ago

mag - mag 3.2.0 - Salmon Salmon

`Added`

#674 - Added --longread_adaptertrimming_tool Where user can chose between porechop_abi (default) and porechop (added by @muabnezor)

`Changed`

#674 - Changed to porechop-abi as default adapter trimming tool for long reads. User can still use porechop if preferred (added by @muabnezor)
#666 - Update SPAdes to version 4.0.0, replace both METASPADES and MEGAHIT with official nf-core modules (requested by @elsherbini, fix by @jfy133)
#666 - Update URLs to GTDB database downloads due to server move (reported by @Jokendo-collab, fix by @jfy133)
#695 - Updated to nf-core 3.0.2 TEMPLATE (by @jfy133)
#695 - Switch more stable Zenodo link for CheckM data (by @jfy133)

`Fixed`

#674 - Make longread preprocessing a subworkflow (added by @muabnezor)
#674 - Add porechop and filtlong logs to multiqc (added by @muabnezor)
#674 - Change local filtlong module to the official nf-core/filtlong module (added by @muabnezor)
#690 - MaxBin2 now using the abundance information from different samples rather than an average (reported by @uel3 and fixed by @d4straub)
#698 - Updated prodigal module to not pick up input symlinks for compression causing pigz errors (reported by @zackhenny, fix by @jfy133 )

`Dependencies`

| Tool | Previous version | New version | | ------------ | ---------------- | ----------- | | Porechop_ABI | | 0.5.0 | | Filtlong | 0.2.0 | 0.2.1 | | SPAdes | 3.15.3 | 4.0.0 |

- Nextflow
Published by jfy133 over 1 year ago

mag - mag 3.1.0 - Pink Panda

[!CAUTION] This release contains a potentially 'breaking change' for some users. The --gtdbtk_pplacer_scratch flag has been replaced with --gtdbtk_pplacer_useram. Check the parameter documentation for more details.

`Added`

#665 - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
#670 - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)

`Changed`

#664 - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
#676 - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)

`Fixed`

#667 - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
#670 - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133)
#672 - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)

`Dependencies`

| Tool | Previous version | New version | | ------ | ---------------- | ----------- | | GTDBTk | 2.3.2 | 2.4.0 |

`Deprecated`

#670 - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)

- Nextflow
Published by jfy133 over 1 year ago

mag - 3.0.3 [2024-08-27]

`Fixed`

#648 - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites)
#646 - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites).
#639 - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan)
#651 - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357)
#652 - Fix documentation typo in using user-defined assembly parameters (reported and fixed by @amizeranschi)
#653 - Fix overwriting of per-bin 'raw' GUNC RUN output files (multi-bin summary tables not affected) (reported by @zackhenny and fixed by @jfy133)

- Nextflow
Published by jfy133 over 1 year ago

mag - 3.0.2 [2024-07-04]

`Changed`

#633 - Changed BUSCO to use offline mode when the database is specified by the user (reported by @ChristophKnapp and many others, fix by @jfy133)
#632 - Use default NanoLyse log of just removed reads rather than custom (by @jfy133)

`Fixed`

#630 - Fix CONCOCT empty bins killing the pipeline, and allow for true multithreading again (removing OPENBLAS loop) (reported by @maxibor, fix by @maxibor and @jfy133)

`Dependencies`

| Tool | Previous version | New version | | -------- | ---------------- | ----------- | | Porechop | 0.2.3_seqan2.1.1 | 0.2.4 | | NanoPlot | 1.26.3 | 1.41.6 | | NanoLyse | 1.1.0 | 1.2.0 |

- Nextflow
Published by jfy133 over 1 year ago

mag - mag 3.0.1

`Changed`

#625 - Updated link to geNomad database for downloading (reported by @amizeranschi, fix by @jfy133)

`Fixed`

#618 - Fix CENTRIFUGE mkfifo failures by using work directory /tmp (reported by @skrakau, fix by @jfy133)

`Dependencies`

| Tool | Previous version | New version | | ---------- | ---------------- | ----------- | | Centrifuge | 1.0.4_beta | 1.0.4.1 |

- Nextflow
Published by jfy133 over 1 year ago

mag - mag 3.0.0 - Magenta Magpie

[!CAUTION] This release contains a potentially 'breaking change' for some users. The pipeline no longer directly accepts FASTQ files via --input. You must use a samplesheet and specify the FASTQs there.

`Added`

#615 - Add new logo (by @jfy133)

`Changed`

#599 - Update to nf-core v2.13.1 TEMPLATE (by @jfy133)
#614 - Update to nf-core v2.14.1 TEMPLATE (by @jfy133)

`Fixed`

#606 - Prevent pipeline crash when premade mashdb given to or no alignments found with GTDB-TK_CLASSIFYWF (reported by @cedwardson4, fix by @jfy133)

`Deprecated`

#599 - Direct reads input (--input 'sample_{R1,R2}.fastq.gz') is no longer supported, all input must come via samplesheets (by @jfy133)

- Nextflow
Published by jfy133 almost 2 years ago

mag - mag 2.5.4

`Changed`

#581 - Added explicit licence text to headers of all custom scripts (reported by @FriederikeHanssen and @maxibor, fix by @jfy133)

`Fixed`

#583 - Fix GTDB database input when directory supplied (fix by @jfy133)

- Nextflow
Published by jfy133 about 2 years ago

mag - mag 2.5.3

`Changed`

#575 - Deactivated MetaSPAdes, Centrifuge, and GTDB in test_full profile due to some container incompatibilities in nf-core megatest AWS configurations (by @jfy133)

`Fixed`

#574 - Fix wrong channel going to BIN_SUMMARY (fix by @maxibor)

- Nextflow
Published by jfy133 about 2 years ago

mag - mag 2.5.2

`Added`

#562 - Add CAT summary into the global bin_summary (by @maxibor)
#565 - Add warning of empty GTDB-TK results if no contigs pass completeness filter (by @jfy133 and @maxibor)

`Changed`

#563 Update to nf-core v2.12 TEMPLATE (by @CarsonJM)
#566 - More logical ordering of MultiQC sections (assembly and bin sections go together respectively) (fix by @jfy133)

`Fixed`

#548 - Fixes to (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor)
- GTDBK-TK execution
- CAT/QUAST/DEPTH bin summary file name collisions
- BUSCO database parsing
- Correct CAT name files
#558 - Fix bug in run merging when dealing with single end data (reported by @roberta-davidson, fix by @jfy133)

- Nextflow
Published by jfy133 about 2 years ago

mag - mag 2.5.1

`Fixed`

#489 - Fix file name collision clashes for CHECKM, CAT, GTDBTK, and QUAST (reported by @tillenglert and @maxibor, fix by @maxibor)
#533 - Fix glob pattern for publishing MetaBAT2 bins in results (reported by @patriciatran, fix by @jfy133)
#535 - Fix input validation pattern to again allow direct FASTQ input (reported by @lennijusten, @emnilsson, fix by @jfy133, @d4straub, @mahesh-panchal, @nvnieuwk)

`Dependencies`

| Tool | Previous version | New version | | ---- | ---------------- | ----------- | | CAT | 4.6 | 5.2.3 |

`Deprecated`

#536 - Remove custom function with native Nextflow for checking file extension (reported by @d4straub, fix by @jfy133)

- Nextflow
Published by jfy133 over 2 years ago

mag - mag 2.5.0 - Aquamarine Kangaroo

`Added`

#504 - New parameters --busco_db, --kraken2_db, and --centrifuge_db now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).

`Changed`

#511 - Update to nf-core 2.10 TEMPLATE (by @jfy133)
#504 - --save_busco_reference is now replaced by --save_busco_db (by @gregorysprenger).

`Fixed`

#514 - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
#515 - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
#516 - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
#520 - Fix missing Tiara output files (fix by @jfy133)
#522 - Fix 'nulls' in depth plot PNG files (fix by @jfy133)

`Deprecated`

#504 - --busco_reference, --busco_download_path, --save_busco_reference parameters have been deprecated and replaced with new parameters (by @gregorysprenger).

- Nextflow
Published by jfy133 over 2 years ago

mag - mag 2.4.0 - Grey Hammerhead

`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 |

- Nextflow
Published by jfy133 over 2 years ago

mag - mag 2.3.2

`Fixed`

#461 - Fix full-size AWS test profile paths (by @jfy133)
#461 - Fix pyDamage results being overwritten (reported by @alexhbnr, fix by @jfy133)

- Nextflow
Published by jfy133 over 2 years ago

mag - mag 2.3.1

`Fixed`

#458 - Correct the major issue in ancient DNA workflow of binning refinement being performed on uncorrected contigs instead of aDNA consensus recalled contigs (issue #449)
#451 - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in #458 )

- Nextflow
Published by jfy133 over 2 years ago

mag - mag 2.3.0 - Red Cow

`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 skipclipping parameter to skip read preprocessing with fastp or adapterremoval. Running the pipeline with skipclipping, keepphix and without specifying a host genome or fasta file skips the FASTQCTRIMMED process (by @prototaxites)
#365 - Added CONCOCT as an additional (optional) binning tool (by @jfy133)
#366 - Added CATSUMMARISE process and catofficial_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 BUSCOPLOT process (previously generated `*.buscofigure.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 |

- Nextflow
Published by jfy133 almost 3 years ago

mag - mag 2.2.1

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

See full CHANGELOG for more information

- Nextflow
Published by jfy133 over 3 years ago

mag - mag 2.2.0 - Golden Mammoth

Restructure binning subworkflow in preparation for aDNA workflow and extended binning
Add ancient DNA subworkflow
Add MaxBin2 as second contig binning tool
Add AdapterRemoval2 as an alternative read trimmer
Add DAS Tool for bin refinement
Activate pipeline-specific institutional nf-core/configs
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
Updated some software: fastp 0.20.1 > 0.23.2, MultiQC 1.9 > 1.12
Fix several bugs

See full CHANGELOG for more information

Contributors

@skrakau @d4straub @jfy133 @maxibor @alexhbnr @pcantalupo

- Nextflow
Published by jfy133 over 3 years ago