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423d2cf
Update metabat2
dialvarezs Aug 22, 2025
ea49e63
Fix BUSCO version in changelog
dialvarezs Aug 22, 2025
ddac1be
Fix metabat2 snaps
dialvarezs Aug 22, 2025
2fce6a9
Add new nf-test configs
dialvarezs Aug 25, 2025
0c671c9
Old config cleanup
dialvarezs Aug 25, 2025
b6934ea
Update changelog
dialvarezs Aug 25, 2025
afac435
Use large disk to prevent storage issues
dialvarezs Sep 5, 2025
ff76d4f
Add missing versions mixing and move version calls after each module …
jfy133 Aug 22, 2025
abd671f
Final version fixes and moving
jfy133 Aug 22, 2025
743e6ae
Update CHANGELOG
jfy133 Aug 22, 2025
d292e39
Update subworkflows/local/assembly_longread/main.nf
jfy133 Aug 22, 2025
32a746c
Replace sceond long ternary with proper if-else
jfy133 Aug 22, 2025
ccceab3
Remove if/else statement and revert to ternary because cannot otherwi…
jfy133 Aug 22, 2025
c476a2e
Remove `.first()` from everywhere as not necessary and can mess with …
jfy133 Aug 22, 2025
140335d
Revert "Remove `.first()` from everywhere as not necessary and can me…
jfy133 Aug 22, 2025
6298686
Correctly remove `.first()` from everywhere as not necessary and can …
jfy133 Aug 22, 2025
7e07848
Use simplified corutils version catch from @mahesh-panchal
jfy133 Aug 22, 2025
0928873
Fix wrong version placement
jfy133 Aug 22, 2025
c8f41e5
Use correct flags for flye and update some snapshots
jfy133 Aug 25, 2025
2ef408e
Typo fix for metaMDG option
jfy133 Aug 25, 2025
8aa3112
Fix autoformatting
jfy133 Aug 25, 2025
7c2aa9d
Use correc tyaml
jfy133 Aug 25, 2025
f8875f0
Update snapshots
dialvarezs Aug 26, 2025
e6c346c
Add multiqc snapshots
dialvarezs Aug 26, 2025
895962c
Update hybrid
dialvarezs Aug 26, 2025
b953b06
Update snapshots
dialvarezs Aug 26, 2025
6362a31
Update snapshot
dialvarezs Aug 26, 2025
f8d6122
Standardise header sand tags
jfy133 Aug 28, 2025
5bd4245
Use porechop_porechop in test_hbyrid profile
jfy133 Aug 28, 2025
1794ac8
update snapshot to include correct tool
jfy133 Aug 28, 2025
0ec5a2d
Add assembly input nf-test (WIP)
dialvarezs Sep 3, 2025
47377d5
Add metaeuk
dialvarezs Sep 3, 2025
70a1b30
Update fastp
dialvarezs Aug 26, 2025
ceff9d8
Update bcftools
dialvarezs Aug 26, 2025
da41a21
Update adapterremoval
dialvarezs Aug 26, 2025
66c0788
Update dastool
dialvarezs Aug 26, 2025
23ad784
Update freebayes
dialvarezs Aug 26, 2025
1b15f5f
Update gtdbtk
dialvarezs Aug 26, 2025
528ea94
Update porechop
dialvarezs Aug 26, 2025
f70c1e3
Improve bcftools usage
dialvarezs Aug 26, 2025
099bd49
Update genomad
dialvarezs Aug 26, 2025
7b7d7a2
Update snapshots
dialvarezs Aug 26, 2025
a7dcec1
Update changelog
dialvarezs Aug 26, 2025
3ed6756
Update porechop/abi to patched version to not result in duplicated reads
jfy133 Aug 25, 2025
1b3cf72
Update CHANGELOG.md
jfy133 Sep 3, 2025
d6a4183
Update nf-schema to stop all params being reported as erroring out
jfy133 Sep 5, 2025
9eee06e
Fix URL typo
jfy133 Sep 5, 2025
ae83d47
Fix typo in github handlge
jfy133 Sep 5, 2025
0ecc217
Fix typo in github handlge
jfy133 Sep 5, 2025
3e48bdc
Add HiRSE code promo badge
jfy133 Sep 5, 2025
d3d4801
Fix RO create
jfy133 Sep 5, 2025
cdcb6c9
Enable GUNC
dialvarezs Sep 5, 2025
177a304
Update assembly_input test
dialvarezs Sep 12, 2025
8175693
Update snapshots (nextflow version)
dialvarezs Sep 12, 2025
4328a79
Update metaeuk config
dialvarezs Sep 12, 2025
1e042f6
Revert to fasta input for metaeuk
dialvarezs Sep 13, 2025
c2b7793
Update changelog
dialvarezs Sep 13, 2025
a39933e
Fix nextflow version
dialvarezs Sep 13, 2025
f45ada3
Fix version pattern capture
jfy133 Sep 15, 2025
1f27cf9
Enable metauk using swissprot + refined bins only
dialvarezs Sep 16, 2025
302bdce
Update CHANGELOG.md
dialvarezs Sep 16, 2025
67d12a8
Update snapshots
dialvarezs Sep 16, 2025
08f440e
Bump version using nf-core tools
jfy133 Sep 17, 2025
2b7d4ca
Update metromap, deprecate old diagram, use metromap in README
jfy133 Sep 17, 2025
e5739e6
nicer HiRSE badge
jfy133 Sep 17, 2025
c170112
Fix ro crate REAMDE change
jfy133 Sep 17, 2025
9f9e169
[automated] Fix code linting
nf-core-bot Sep 17, 2025
f414caa
Remove short-read profiling from metormap
jfy133 Sep 17, 2025
88dcdfe
Update all snapshots to include latest pipeline version, standarding …
jfy133 Sep 17, 2025
c3e09a4
Update snapshots
dialvarezs Sep 17, 2025
64124a0
Update snapshot
dialvarezs Sep 18, 2025
4181f14
Increase shards
dialvarezs Sep 18, 2025
2dc74dd
Update GTDBK to version that works with conda
jfy133 Sep 19, 2025
9b4f24f
update CHANGELOG
jfy133 Sep 19, 2025
99175d0
Fix GTDBTK version in snapshot
jfy133 Sep 19, 2025
1d1aa60
Update docs/usage.md
jfy133 Sep 19, 2025
7d53d7a
Address comments from @erikrikarddaniel
jfy133 Sep 19, 2025
a951cea
Update docs/usage.md
jfy133 Sep 19, 2025
10e90d9
Update docs/usage.md
jfy133 Sep 19, 2025
2650a55
Update chagnelog date and metromap modifications after feedback from …
jfy133 Sep 19, 2025
4372095
update snapshot
jfy133 Sep 19, 2025
b313b6b
Improve CONDA pinning in several modules to match snapshot and ensure…
jfy133 Sep 21, 2025
8d0d0fc
bump NANOPLOT to 1.46.1 to fix kaleodio issue in conda
jfy133 Sep 21, 2025
f7b1133
Bump NANOPLOT versions in snaphost
jfy133 Sep 21, 2025
b56a595
Use correct repository
jfy133 Sep 21, 2025
14a87bb
Update CONCOCT to use latest conda build and fix version reporting
jfy133 Sep 21, 2025
48cd6d4
Update all snapshots fror hardcoded coreuttlis
jfy133 Sep 22, 2025
a41a22b
Syncronise local rename modules to match container of UNTAR module (t…
jfy133 Sep 22, 2025
4fb559e
Fix GTDBTK DB prep
jfy133 Sep 22, 2025
45807f7
And for single end
jfy133 Sep 22, 2025
32de7db
Use correct version for update coreutrils capture
jfy133 Sep 22, 2025
46f1882
Remove quotes to make snapshot
jfy133 Sep 22, 2025
258edb8
Remove quotes everywehere for the coreutils
jfy133 Sep 22, 2025
0b4055b
Standardise remaining core utils conda/containers and update snapshots
jfy133 Sep 23, 2025
67e285b
Update hybrid snapshot too
jfy133 Sep 23, 2025
840b03e
Use same container not just conda env for coreutils (to match with of…
jfy133 Sep 23, 2025
0278a1b
Remove variable MultiQC YAML files in longread only test
jfy133 Sep 23, 2025
e33a205
Use correct versions in snapshots for all TAR processes
jfy133 Sep 23, 2025
9d3b6d5
Deprecate GDTBTK's --gtdb_mash parameter as no longer suppoted by the…
jfy133 Sep 23, 2025
c9ff54e
Revert "Deprecate GDTBTK's --gtdb_mash parameter as no longer suppote…
jfy133 Sep 23, 2025
9f691c9
Re-deprecate mash_db bit retain -skip_ani_screen in GTDBTk process
jfy133 Sep 23, 2025
ab9d966
Typo fixes as noticed by @dialvarezs
jfy133 Sep 23, 2025
47f2709
Implement option to skip FastANI screen in GTDB-Tk (to replace mash_d…
jfy133 Sep 23, 2025
7e43d61
Improve parameter name for clarity and add changelog entry
jfy133 Sep 24, 2025
033c2c4
Update nextflow_schema.json
jfy133 Sep 23, 2025
2ada69d
[automated] Fix code linting
nf-core-bot Sep 23, 2025
a451aa5
Deactivate scratch on METASPADES to allow functioning with fusion
jfy133 Sep 24, 2025
e1a77e3
Use the correct Seqera (unofficial) approve from @FriederikeHanssen@e…
jfy133 Sep 24, 2025
3be1a4b
Add missing --threads parameter for metaeuk easypredict
jfy133 Sep 25, 2025
7560fa7
Make sure all custom exit code contiions are consistent, and add igno…
jfy133 Sep 29, 2025
6f0a1bc
Use latest GTDB download link
jfy133 Sep 29, 2025
1424a2c
Use correct URLs for test data samplesheet and GTDB, deactivate CAT d…
jfy133 Sep 29, 2025
634164e
Try CheckM2 instead of BUSCO
jfy133 Sep 30, 2025
550e64a
Update CHANGELOG.md
jfy133 Sep 30, 2025
a252c28
Fix linting (mismtach of schema with config, typo in module name in m…
jfy133 Sep 30, 2025
bc61826
docs(coverage): add section to usage documenting how to tune the perc…
prototaxites Sep 30, 2025
6bebd69
fix(test_full): set longread_percentidentity to 85
prototaxites Sep 30, 2025
b8cfe5f
docs: update changelog
prototaxites Sep 30, 2025
c3524ae
lint: trailing whitespace
prototaxites Sep 30, 2025
80e98d7
feat: post-release version bump
prototaxites Sep 30, 2025
c88532b
fix: bump pipeline version in all snapshots
prototaxites Sep 30, 2025
b324244
Apply suggestions from code review
prototaxites Sep 30, 2025
a09c114
added TODOs so i don't forget any
harper357 Oct 6, 2025
f49249a
added "enable_{tool)" for binqc
harper357 Oct 6, 2025
fb4caea
added enable_{tool} parameters with enable_busco as true as default
harper357 Oct 6, 2025
71d8e74
updated modules and their imports
harper357 Oct 6, 2025
554b595
fixed relative import
harper357 Oct 6, 2025
60b45a8
changed main variables
harper357 Oct 6, 2025
f72f075
support for checkm
harper357 Oct 6, 2025
6dd30ff
support for checkm2
harper357 Oct 6, 2025
c01cdba
hotfix for checkm support
harper357 Oct 6, 2025
3c9b6a3
busco support
harper357 Oct 6, 2025
9222c6d
remove TODOs
harper357 Oct 6, 2025
f9d95b9
updated TODO and changed to qc_summaries
harper357 Oct 7, 2025
e39661d
Merge branch 'dev' into multiple_bin_qc
jfy133 Oct 7, 2025
2bd856e
Rename bin QC tool parameters for consistency with other parameters
jfy133 Oct 14, 2025
1c84de1
Update binQC to export BUSCO, CheckM, and CheckM2 summaries separatel…
jfy133 Oct 14, 2025
3b8068f
update combine_tables.py to merge all files
jfy133 Oct 14, 2025
797278a
Update CHANGELOG
jfy133 Oct 14, 2025
f14f167
Add suffixes, improve changelog and update output.md to better descri…
jfy133 Oct 14, 2025
a60ab1c
Fix when not all bin qc tools are executed
jfy133 Oct 14, 2025
beac2e4
Update GTDBTK local subworkflow to filter on any/all bin QC metrics a…
jfy133 Oct 15, 2025
fbecbb7
Use correct variable name for renaming GTDBTK results
jfy133 Oct 15, 2025
833da83
Merge branch 'dev' into multiple_bin_qc
jfy133 Oct 15, 2025
8be3e60
Update snapshots for working tests
jfy133 Oct 15, 2025
5631752
Merge branch 'multiple_bin_qc' of github.com:harper357/mag into multi…
jfy133 Oct 15, 2025
80f1dc8
add MetaBinner
d4straub Oct 16, 2025
213e20a
[automated] Fix code linting
nf-core-bot Oct 16, 2025
e5cbdc7
merge dev
d4straub Oct 17, 2025
0f6b11d
Debugging backup
jfy133 Oct 17, 2025
6665f6e
add script to bin
d4straub Oct 17, 2025
bbdc652
Simplify code
jfy133 Oct 17, 2025
02748f3
Merge branch 'dev' into multiple_bin_qc
jfy133 Oct 17, 2025
838015d
Apply suggestions from code review
jfy133 Oct 17, 2025
0cb4010
Update code to correctly append extension to bin names in GTDB-Tk sub…
jfy133 Oct 17, 2025
64328a8
Merge branch 'multiple_bin_qc' of github.com:harper357/mag into multi…
jfy133 Oct 17, 2025
a165949
Activate busco clean to remove variable intermediate files
jfy133 Oct 17, 2025
3aeaecf
Ignore variable md5sums and names only
jfy133 Oct 17, 2025
5127543
Allow duplicats because multiple QC tools per bin
jfy133 Oct 21, 2025
4f5605b
adjust create_metabinner_bins.py usage
d4straub Oct 22, 2025
ca18a82
Set skip_aniscreen to all test configs in case gtdbtk tested with the…
jfy133 Oct 22, 2025
9faebcc
Retain bins based on completeness if any of the bin qc tools report h…
jfy133 Oct 22, 2025
8230584
update metabinner output
d4straub Oct 22, 2025
baab236
refine metabinner output
d4straub Oct 22, 2025
948c3a1
adjust metabinner bin filenames
d4straub Oct 22, 2025
9e4a2cd
adjust metabinner bin file names again
d4straub Oct 22, 2025
6dc9a85
update file publishing, testing, and docs
d4straub Oct 22, 2025
471c9b9
--fix rocrate_readme_sync
d4straub Oct 22, 2025
6f98ee2
ignore metabinner error 1 and 255 and add acknowledgment
d4straub Oct 23, 2025
33eddd5
merge from dev
d4straub Oct 24, 2025
a78e110
fix rocrate_readme_sync
d4straub Oct 24, 2025
89e30e9
Update docs/output.md
d4straub Oct 24, 2025
9b0032c
add param bin_metabinner_scale
d4straub Oct 24, 2025
4332440
handle tool version appropriately
d4straub Oct 24, 2025
5d68eb1
update CHANGELOG with acknowledgment
d4straub Oct 24, 2025
41f32b7
merge in dev
d4straub Oct 24, 2025
34ac949
fix rocrate_readme_sync
d4straub Oct 24, 2025
ae187a0
split METABINNER into subworkflow
d4straub Oct 27, 2025
7c54b53
Post release version bump
jfy133 Oct 27, 2025
e28c2cd
Bump version in snapshots
jfy133 Oct 27, 2025
f4fd367
Merge pull request #895 from nf-core/post-5.1.0-bump
jfy133 Oct 28, 2025
fbbf820
merge upstream dev
d4straub Oct 28, 2025
04c9e50
fix rocrate_readme_sync
d4straub Oct 28, 2025
20175a9
Remove obsolete command
dialvarezs Oct 28, 2025
fc4f2ee
Update changelog
dialvarezs Oct 28, 2025
a8b4488
Update ROcrate
jfy133 Oct 28, 2025
e5ebf2e
Merge pull request #896 from dialvarezs/fix-readme
dialvarezs Oct 28, 2025
ea45b72
Try workaround to get AWS full tests to work
jfy133 Oct 29, 2025
6fa6c98
Merge branch 'dev' into multiple_bin_qc
jfy133 Oct 29, 2025
957996c
Update subworkflows/local/gtdbtk/main.nf
jfy133 Oct 29, 2025
b22cfdc
[automated] Fix code linting
nf-core-bot Oct 29, 2025
6c1ea5c
Apply suggestion from @jfy133
jfy133 Oct 29, 2025
5aadd97
Update test_full.config
jfy133 Oct 29, 2025
fed6087
Apply suggestion from @jfy133
jfy133 Oct 29, 2025
8d12c6f
include COMEBin in dastool/bins output folder
AlexHoratio Oct 31, 2025
a4b6445
Update CHANGELOG.md
AlexHoratio Oct 31, 2025
0aa9ab4
Update README.md
AlexHoratio Oct 31, 2025
596f0ae
replace glob
AlexHoratio Oct 31, 2025
9e65579
Update CHANGELOG.md
AlexHoratio Oct 31, 2025
981c8f8
Apply suggestion from @dialvarezs
d4straub Nov 3, 2025
3e689bc
Apply suggestion from @dialvarezs
d4straub Nov 3, 2025
17fd583
apply suggestions from code review
d4straub Nov 3, 2025
ebb2f12
merge upstream dev
d4straub Nov 3, 2025
a4943f9
fix rocrate_readme_sync
d4straub Nov 3, 2025
587cfce
[automated] Fix code linting
nf-core-bot Nov 3, 2025
5b262fb
Update single_end test basic snapshot to include GTDBTk
jfy133 Nov 3, 2025
82064fa
update test_alternatives basic snapshot too
jfy133 Nov 3, 2025
044788b
Simplify error message
jfy133 Nov 3, 2025
1880a9c
Auto format
jfy133 Nov 3, 2025
faddd5a
Merge pull request #842 from harper357/multiple_bin_qc
jfy133 Nov 3, 2025
05523f4
Merge pull request #906 from nf-core/full_test_fix_5_1
jfy133 Nov 3, 2025
7b42f6e
Update description field in ro-crate-metadata.jsonUpdate RO crate
jfy133 Nov 3, 2025
4df9f81
Merge pull request #907 from AlexHoratio/dev
prototaxites Nov 3, 2025
89e6557
Update to new runner size syntax
mashehu Nov 3, 2025
46f8068
Merge pull request #910 from nf-core/mashehu-patch-1
mashehu Nov 3, 2025
c9b49d3
Update get_mag_depths.py to ensure column ordering
dialvarezs Nov 4, 2025
79dae93
Update CHANGELOG
dialvarezs Nov 4, 2025
bc63970
Fix multiple sequencing platform validation when using binning_map_mo…
dialvarezs Nov 4, 2025
b8f946a
Update changelog
dialvarezs Nov 4, 2025
87ca9ec
Update changelog
dialvarezs Nov 4, 2025
c5fd6b9
Update bin/get_mag_depths.py
dialvarezs Nov 4, 2025
bb77ce6
Merge pull request #911 from dialvarezs/fix-depth-columns
dialvarezs Nov 4, 2025
cb8ee67
Merge branch 'dev' into fix-platform-validation
dialvarezs Nov 4, 2025
59ec728
Bump version
dialvarezs Nov 4, 2025
ae86278
Fix changelog
dialvarezs Nov 4, 2025
dfb2e07
clean up unzipped file
d4straub Nov 4, 2025
33f87a5
merge upstream dev
d4straub Nov 4, 2025
0ab6474
fix rocrate_readme_sync
d4straub Nov 4, 2025
8f432dd
min_contig_size now via process input val instead of task.ext.
d4straub Nov 4, 2025
0e7cb3d
Snapshots
dialvarezs Nov 4, 2025
83a108c
Fix ordering
dialvarezs Nov 4, 2025
5336881
Exclude busco_summary
dialvarezs Nov 4, 2025
b60e1f6
Merge pull request #912 from dialvarezs/fix-platform-validation
dialvarezs Nov 4, 2025
d8783b1
Merge remote-tracking branch 'upstream/dev' into prerelease-version-b…
dialvarezs Nov 4, 2025
96da27f
Merge remote-tracking branch 'upstream/dev' into add-MetaBinner
dialvarezs Nov 4, 2025
5c4f4b8
Merge pull request #881 from d4straub/add-MetaBinner
d4straub Nov 4, 2025
5af8bf4
Merge remote-tracking branch 'upstream/dev' into prerelease-version-b…
dialvarezs Nov 4, 2025
7cc714c
Fix rocrate
dialvarezs Nov 4, 2025
ddb8c81
Include names in changelog
dialvarezs Nov 4, 2025
7d0fe05
Updated metro maps by @jfy133
dialvarezs Nov 5, 2025
6a848cd
Merge pull request #913 from dialvarezs/prerelease-version-bump-5.2.0
dialvarezs Nov 5, 2025
789b0f6
Update genomad modules
dialvarezs Nov 6, 2025
ba695d7
Merge pull request #918 from dialvarezs/update-genomad
jfy133 Nov 6, 2025
d8b2f87
Update release announcement action
dialvarezs Nov 6, 2025
4c7ac9d
Merge pull request #919 from dialvarezs/update-actions
dialvarezs Nov 6, 2025
69ad3e3
Fix BUSCO publishing
dialvarezs Nov 6, 2025
714d9f0
Update CHANGELOG
dialvarezs Nov 6, 2025
053cd4d
Merge pull request #921 from dialvarezs/fix-busco-publishing
dialvarezs Nov 6, 2025
64caac5
Apply review suggestions
dialvarezs Nov 7, 2025
b04a935
Merge pull request #922 from dialvarezs/review-suggestions
dialvarezs Nov 7, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/nf-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ jobs:
runs-on: # use self-hosted runners
- runs-on=${{ github.run_id }}-nf-test
- runner=4cpu-linux-x64
- disk=large
- volume=80gb
strategy:
fail-fast: false
matrix:
Expand Down
2 changes: 1 addition & 1 deletion .nf-core.yml
Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,4 @@ template:
name: mag
org: nf-core
outdir: .
version: 5.1.0
version: 5.2.0
88 changes: 59 additions & 29 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,37 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v5.1.0 - 2025-10-27
## v5.2.0 - Puce Pangolin [2025-11-07]

### `Added`

- [#842](https://github.com/nf-core/mag/pull/842) - Add support for running multiple binQC tools in one run using dedicated `--run_busco`, `--run_checkm`, and `--run_checkm2` parameters (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
- [#881](https://github.com/nf-core/mag/pull/881) - Add binner MetaBinner (by @d4straub, insprired by @HeshamAlmessady & @AlphaSquad)

### `Changed`

- [#842](https://github.com/nf-core/mag/pull/842) - Change `bin_summary.tsv` format for improved clarity and more comprehensiveness (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)
- Now will include columns from all bin QC tools executed in a given run (i.e., all/any of BUSCO, CheckM and CheckM2)
- Adds suffixes to all columns (`_<toolname>`) to distinguish which column comes from which tool

### `Fixed`

- [#896](https://github.com/nf-core/mag/pull/896) - Remove obsolete execution command from README (by @dialvarezs)
- [#907](https://github.com/nf-core/mag/pull/907) - Include refined bins from all binners in the `DASTool/bins` output folder (by @AlexHoratio)
- [#911](https://github.com/nf-core/mag/pull/911) - Ensure column order is consistent when generating depth summaries to prevent swapped results on merged depth summary (by @dialvarezs)
- [#912](https://github.com/nf-core/mag/pull/912) - Fix validation of multiple sequencing platforms when using `binning_map_mode = "all"` (reported by @mjfi2sb3, fix by @dialvarezs)

### `Dependencies`

| Tool | Previous version | New version |
| ---------- | ---------------- | ----------- |
| MetaBinner | | 1.4.4-0 |

### `Deprecated`

- [#842](https://github.com/nf-core/mag/pull/842) - Remove `--binqc_tool` (by @harper357, with contributions from @dialvarezs, @prototaxites and @jfy133)

## v5.1.0 - Platinum Pudu [2025-10-27]

### `Added`

Expand All @@ -30,7 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 5.0.0 - [2025-09-30]
## v5.0.0 - Green Squirrel [2025-09-30]

### `Added`

Expand Down Expand Up @@ -102,7 +132,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#855](https://github.com/nf-core/mag/pull/855) - Remove test_adapterremoval, test_ancient_dna, test_bbnorm, test_busco_auto, test_host_rm, test_hybrid_host_rm, test_binrefinement, test_concoct and test_longread profiles (added by @dialvarezs)
- [#864](https://github.com/nf-core/mag/pull/864) - Remove `--gtdb_mash` due to dropping of support by GTDBTk itself (by @prototaxites and @jfy133)

## v4.0.0 - [2025-05-22]
## v4.0.0 - Blue Huemul [2025-05-22]

### `Added`

Expand Down Expand Up @@ -138,7 +168,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#730](https://github.com/nf-core/mag/pull/730) - Remove `--busco_auto_lineage_prok` due to update and simplified usage of BUSCO (added by @jfy133, @dialvarezs)

## 3.4.0 [2025-04-04]
## v3.4.0 - Green Gecko [2025-04-04]

### `Added`

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### `Deprecated`

## 3.3.0 [2024-12-19]
## v3.3.0 - Red Reindeer [2024-12-19]

### `Added`

Expand Down Expand Up @@ -222,7 +252,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 3.2.1 [2024-10-30]
## v3.2.1 [2024-10-30]

### `Added`

Expand All @@ -236,7 +266,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 3.2.0 [2024-10-27]
## v3.2.0 - Salmon Salmon [2024-10-27]

### `Added`

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### `Deprecated`

## 3.1.0 [2024-10-04]
## v3.1.0 - Pink Panda [2024-10-04]

### `Added`

Expand Down Expand Up @@ -296,7 +326,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated `--gtdbtk_pplacer_scratch` due to unintuitive usage (reported by harper357, fixed by @jfy133)

## 3.0.3 [2024-08-27]
## v3.0.3 [2024-08-27]

### `Added`

Expand All @@ -315,7 +345,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 3.0.2 [2024-07-04]
## v3.0.2 [2024-07-04]

### `Added`

Expand All @@ -338,7 +368,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 3.0.1 [2024-06-10]
## v3.0.1 [2024-06-10]

### `Added`

Expand All @@ -358,7 +388,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 3.0.0 - [2024-05-13]
## v3.0.0 - Magenta Magpie [2024-05-13]

### `Added`

Expand All @@ -379,7 +409,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#599](https://github.com/nf-core/mag/pull/599) - Direct reads input (`--input 'sample_{R1,R2}.fastq.gz'`) is no longer supported, all input must come via samplesheets (by @jfy133)

## 2.5.4 - [2024-02-12]
## v2.5.4 [2024-02-12]

### `Added`

Expand All @@ -396,7 +426,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 2.5.3 - [2024-02-05]
## v2.5.3 [2024-02-05]

### `Added`

Expand All @@ -412,7 +442,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 2.5.2 - [2024-02-02]
## v2.5.2 [2024-02-02]

### `Added`

Expand All @@ -437,7 +467,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Deprecated`

## 2.5.1 - [2023-11-17]
## v2.5.1 [2023-11-17]

### `Added`

Expand All @@ -459,7 +489,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#536](https://github.com/nf-core/mag/pull/536) - Remove custom function with native Nextflow for checking file extension (reported by @d4straub, fix by @jfy133)

## 2.5.0 - [2023-10-10]
## 2.5.0 - Aquamarine Kangaroo - [2023-10-10]

### `Added`

Expand All @@ -484,7 +514,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_reference`, `--busco_download_path`, `--save_busco_reference` parameters have been deprecated and replaced with new parameters (by @gregorysprenger).

## 2.4.0 - 2023-09-26
## v2.4.0 - Grey Hammerhead [2023-09-26]

### `Added`

Expand Down Expand Up @@ -548,7 +578,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#458](https://github.com/nf-core/mag/pull/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](https://github.com/nf-core/mag/issues/449))
- [#451](https://github.com/nf-core/mag/pull/451) - Fix results file overwriting in Ancient DNA workflow (reported by @alexhbnr, fix by @jfy133, and integrated by @maxibor in [#458](https://github.com/nf-core/mag/pull/458) )

## v2.3.0 - [2023/03/02]
## v2.3.0 - Red Cow [2023-03-02]

### `Added`

Expand Down Expand Up @@ -585,7 +615,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| Freebayes | 1.3.5 | 1.3.6 |
| SAMtools | 1.15 | 1.16.1 |

## v2.2.1 - 2022/08/25
## v2.2.1 [2022-08-25]

### `Added`

Expand All @@ -598,7 +628,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Dependencies`

## v2.2.0 - 2022/06/14
## v2.2.0 - Golden Mammoth [2022-06-14]

### `Added`

Expand Down Expand Up @@ -631,7 +661,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| fastp | 0.20.1 | 0.23.2 |
| MultiQC | 1.11 | 1.12 |

## v2.1.1 - 2021/11/25
## v2.1.1 [2021-11-25]

### `Added`

Expand All @@ -654,7 +684,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#255](https://github.com/nf-core/mag/pull/255) - Update gtdbtk conda channel.
- [#258](https://github.com/nf-core/mag/pull/258) - FastP results are now in MultiQC.

## v2.1.0 - 2021/07/29
## v2.1.0 - Black Zebra [2021-07-29]

### `Added`

Expand All @@ -670,7 +700,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#226](https://github.com/nf-core/mag/pull/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
## v2.0.0 - Silver Swan [2021-06-01]

### `Added`

Expand Down Expand Up @@ -705,7 +735,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#195](https://github.com/nf-core/mag/pull/195) - Fix documentation regarding required compression of input FastQ files [#160](https://github.com/nf-core/mag/issues/160)
- [#196](https://github.com/nf-core/mag/pull/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](https://github.com/nf-core/mag/issues/90), [#188](https://github.com/nf-core/mag/issues/188)

## v1.2.0 - 2021/02/10
## v1.2.0 - Yellow Squirrel [2021-02-10]

### `Added`

Expand All @@ -725,7 +755,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#143](https://github.com/nf-core/mag/pull/143) - Change parameter: `--manifest` -> `--input`

## v1.1.2 - 2020/11/24
## v1.1.2 - Blue Panda [2020-11-24]

### `Changed`

Expand All @@ -735,7 +765,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#133](https://github.com/nf-core/mag/pull/133) - Fixed processing of `--input` parameter [#131](https://github.com/nf-core/mag/issues/131)

## v1.1.1 - 2020/11/10
## v1.1.1 - Lime Owl [2020-11-10]

### `Added`

Expand All @@ -752,7 +782,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#120](https://github.com/nf-core/mag/pull/120) - Fix link to CAT database in help message
- [#124](https://github.com/nf-core/mag/pull/124) - Fix description of `CAT` process in `output.md`

## v1.1.0 - 2020/10/06
## v1.1.0 - White Elephant [2020-10-06]

### `Added`

Expand Down Expand Up @@ -797,7 +827,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#29](https://github.com/nf-core/mag/pull/29) - Change depreciated parameters: `--singleEnd` -> `--single_end`, `--igenomesIgnore` -> `--igenomes_ignore`

## v1.0.0 - 2019/12/20
## v1.0.0 - Purple Corgi [2019-12-20]

Initial release of nf-core/mag, created with the [nf-core](http://nf-co.re/) template.

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4 changes: 4 additions & 0 deletions CITATIONS.md
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Expand Up @@ -52,6 +52,10 @@

> Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014). Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), 1144–1146. doi: 10.1038/nmeth.3103

- [MetaBinner](https://doi.org/10.1186/s13059-022-02832-6)

> Wang Z, Huang P, You R, Sun F, Zhu S. MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome Biol. 2023 Jan 6;24(1):1. doi: 10.1186/s13059-022-02832-6. PMID: 36609515; PMCID: PMC9817263.

- [DAS Tool](https://doi.org/10.1038/s41564-018-0171-1)

> Sieber, C. M. K., et al. 2018. "Recovery of Genomes from Metagenomes via a Dereplication, Aggregation and Scoring Strategy." Nature Microbiology 3 (7): 836-43. doi: 10.1038/s41564-018-0171-1
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9 changes: 2 additions & 7 deletions README.md
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Expand Up @@ -47,7 +47,7 @@ The pipeline then:
- performs assembly using [MEGAHIT](https://github.com/voutcn/megahit) and [SPAdes](http://cab.spbu.ru/software/spades/), and checks their quality using [Quast](http://quast.sourceforge.net/quast)
- (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html)
- predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal), and bins with [Prokka](https://github.com/tseemann/prokka) and optionally [MetaEuk](https://www.google.com/search?channel=fs&client=ubuntu-sn&q=MetaEuk)
- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), [CONCOCT](https://github.com/BinPro/CONCOCT), and/or [COMEBin](https://github.com/ziyewang/COMEBin)
- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), [CONCOCT](https://github.com/BinPro/CONCOCT), [COMEBin](https://github.com/ziyewang/COMEBin), and/or [MetaBinner](https://github.com/ziyewang/MetaBinner)
- checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), [CheckM](https://ecogenomics.github.io/CheckM/), or [CheckM2](https://github.com/chklovski/CheckM2) and optionally [GUNC](https://grp-bork.embl-community.io/gunc/)
- Performs ancient DNA validation and repair with [pyDamage](https://github.com/maxibor/pydamage) and [freebayes](https://github.com/freebayes/freebayes)
- optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool)
Expand All @@ -60,12 +60,6 @@ Furthermore, the pipeline creates various reports in the results directory speci
> [!NOTE]
> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.

```bash
nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --outdir <OUTDIR>
```

or

```bash
nextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR>
```
Expand Down Expand Up @@ -107,6 +101,7 @@ Other code contributors include:
- [Nikolaos Vergoulidis](https://github.com/IceGreb)
- [Greg Fedewa](https://github.com/harper357)
- [Vini Salazar](https://github.com/vinisalazar)
- [Alex Caswell](https://github.com/AlexHoratio)

Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)

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2 changes: 1 addition & 1 deletion assets/multiqc_config.yml
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@@ -1,5 +1,5 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/5.1.0" target="_blank">nf-core/mag</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mag/5.1.0/docs/output" target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/5.2.0" target="_blank">nf-core/mag</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/mag/5.2.0/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-mag-methods-description":
order: -1000
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