Release: v5.3.0 Rainbow Rattlesnake by dialvarezs · Pull Request #948 · nf-core/mag

dialvarezs · 2025-12-01T13:07:53Z

`Added`

#905 - Add nf-test snapshot for test_assembly_input profile (by @dialvarezs)
#930 - Add binner SemiBin2 (by @d4straub)
#861 - Added --generate_bigmag_file to execute the bigmag workflow that generates the file to be used as input for BIgMAG (added by @jeffe107)

`Changed`

#932 - Replaced usages of deprecated Channel() with channel() and fix other LSP warnings (by @dialvarezs)
#937 - Updated to nf-core 3.5.1 TEMPLATE (by @dialvarezs)
#938 - Update nf-core modules (by @dialvarezs)

`Fixed`

#894 - Fix read order in metaSPAdes to allow co-assembly of paired-end data of multiple samples (reported by @maartenciers, fix by @jfy133 with contributions from @prototaxites, @d4straub and @dialvarezs)
#927 - MetaBinner now succeeds when no contigs are too short or all are binned (reported by @MicroSeq, fix by @d4straub)
#929 - Allow the domain_classification.R script to run with any assembler, not just Megahit or Spades (reported by @MicroSeq, fix by @prototaxites)
#943 - Fixed concatenation of BUSCO summaries with uneven columns by changing from csvtk to qsv (reported by @jfy133 and @julianu, fix by @dialvarezs)
#943 - Fixed creation of the Tiara report channel used for concatenation (by @dialvarezs)
#945 - Skip mixing of GTDB-Tk MultiQC files when binning is skipped (reported by @amizeranschi, fix by @dialvarezs)
#953 - metaSPAdes retries upon error 250 (out of memory), rather than finishing the pipeline.
#954 - Skip GTDB-Tk when no bin QC tool is enabled and add warning messages (fix by @dialvarezs)
#956 - Support long reads assemblers in assembly input (fix by @dialvarezs)

`Dependencies`

Tool	Previous version	New version
bcftools	1.21	1.22
csvtk	0.31.0
fastp	0.24.0	1.0.1
geNomad	1.11.1	1.11.2
metamdbg	1.1	1.2
mmseqs	17.b804f	18.8cc5c
nf-core		3.5.1
qsv		5.1.0
samtools	1.21	1.22.1
SemiBin2		2.2.0

`Deprecated`

#943 - Remove csvtk/concat module (by @dialvarezs).

Co-authored-by: James A. Fellows Yates <[email protected]>

…es-contain-unequal-number-of-reads

…-unequal-number-of-reads' of github.com:nf-core/mag into 890-metaspades-exit-status-21-paired-read-files-contain-unequal-number-of-reads

dialvarezs · 2025-12-01T17:54:07Z

When using conda, Semibin2 seems to be trying to train a new model... Any ideas why, @d4straub?

d4straub · 2025-12-02T07:27:53Z

When using conda, Semibin2 seems to be trying to train a new model.

Yes that is intentionally. Semibin2 should train a model with not only conda but also singularity & docker. Because pre-trained models are only available for single-bam input and CI test 1 & 3 have multiple bam input. However, I just checked the error report, and the model is trained in just a few seconds. The last message by Semibin2 is SemiBin2[11530] INFO Start binning.. I am not sure though why binning should take longer with conda than singularity/docker.
I re-started the failed tests just to make sure that wasnt some weird coincidence.

Edit:

no, timeout seems reproducible for tests 1 & 3
curious is though that SemiBin2 works for test 4 ('-profile hybrid' ) with conda

Edit2: CI test 4 ('-profile hybrid' ) has a single sample, i.e. model is pre-trained, input only one bam file. Still a mystery why SemiBin2 fails with conda on multiple samples in CI tests.

FriederikeHanssen

Got no additional things. All my comments are merely suggestions. Nice work

Address #948 review comments

dialvarezs · 2025-12-02T15:43:56Z

no, timeout seems reproducible for tests 1 & 3

I can reproduce it locally with conda. It's strange, because when it reaches that point of "Start binning.", CPU usage drops to 0% and stays like that.

I'm going to check the conda vs the container dependencies if I this is because some bad pin.

EDIT: There is an issue that seems to resemble this behaviour: BigDataBiology/SemiBin#208

EDIT 2: I found the issue! Seems to be the igraph package that recently got v1.0.0

Update semibin module

metaSPAdes error 250 (OOM) triggers retry rather than finish

…nabled

Improve handling of GTDB-Tk + Bin QC

Co-authored-by: Diego Alvarez S. <[email protected]>

Support long reads assemblers in assembly input

jeffe107 and others added 30 commits September 16, 2025 18:40

BIgMAG compatibility

105a51b

[automated] Fix code linting

5e430e3

Update docs/output.md

56a200d

Co-authored-by: James A. Fellows Yates <[email protected]>

Update docs/output.md

0168b46

Co-authored-by: James A. Fellows Yates <[email protected]>

Update main.nf

5abd21b

Update main.nf

926d01c

Update main.nf

f5b4502

Update modules/local/bigmag_summary/main.nf

83ae6a0

Co-authored-by: James A. Fellows Yates <[email protected]>

Update modules/local/bigmag_summary/main.nf

7ef95af

Co-authored-by: James A. Fellows Yates <[email protected]>

Update modules/local/bigmag_summary/main.nf

99e5bf8

Co-authored-by: James A. Fellows Yates <[email protected]>

Update bigmag_summary.py

38e48b2

Update usage.md

22517cd

Update nextflow.config

9ca66ae

Update mag.nf

568abc5

Update nextflow_schema.json

d34d2ad

Update CHANGELOG.md

ed196db

Update main.nf

0f3476d

Update meta.yml

bb864fa

Make sure to actually test coassembly

bdf5ac3

Fix input to pooling step to combine reads correctly

f73c635

Document fix

dac9ccd

[automated] Fix code linting

24a456b

Merge branch 'dev' into 890-metaspades-exit-status-21-paired-read-fil…

b033632

…es-contain-unequal-number-of-reads

Correct version in changelog

12f2b25

Merge branch 'dev' into 890-metaspades-exit-status-21-paired-read-fil…

0b327d6

…es-contain-unequal-number-of-reads

Update snapshot to represent pooled (i.e. coassembled) data

3cfcb59

Merge branch '890-metaspades-exit-status-21-paired-read-files-contain…

66b1301

…-unequal-number-of-reads' of github.com:nf-core/mag into 890-metaspades-exit-status-21-paired-read-files-contain-unequal-number-of-reads

test_assembly_input snapshot [WIP]

e7b52eb

test_assembly_input snapshot [WIP]

57f55a3

Keep ordering

7bc845f

dialvarezs added 2 commits December 1, 2025 12:57

Address #948 review comments

f2fdb8c

Style

f7dd196

FriederikeHanssen reviewed Dec 1, 2025

View reviewed changes

Comment thread conf/test_assembly_input.config Outdated

Update comment about BIgMAG

2852171

FriederikeHanssen reviewed Dec 1, 2025

View reviewed changes

Comment thread modules/nf-core/multiqc/main.nf Outdated

dialvarezs added 2 commits December 1, 2025 13:55

Downgrade multiqc to prevent issue

49ec21b

Update snapshots

4b07090

FriederikeHanssen reviewed Dec 2, 2025

View reviewed changes

Comment thread subworkflows/local/tiara/main.nf

FriederikeHanssen approved these changes Dec 2, 2025

View reviewed changes

Merge pull request #949 from dialvarezs/review-fixes

783d3bc

Address #948 review comments

dialvarezs mentioned this pull request Dec 2, 2025

Update semibin/singleeasybin environment nf-core/modules#9495

Merged

17 tasks

dialvarezs and others added 10 commits December 2, 2025 13:49

Update semibin module

5750548

Merge pull request #952 from dialvarezs/update-semibin

f61a474

Update semibin module

METASPAdes error 250 (OOM) triggers retry rather than finish

9003119

Update CHANGELOG.md

3931a42

Merge pull request #953 from AlexHoratio/metaspades_e250

664423a

metaSPAdes error 250 (OOM) triggers retry rather than finish

Add verifications to ensure that GTDB-Tk is only run when bin QC is e…

09db8a9

…nabled

Fix param names, add additional warning

657493c

Fix conditional

1690a26

Update changelog

fea7965

Merge pull request #954 from dialvarezs/fix-gtdbtk-binqc

45119fa

Improve handling of GTDB-Tk + Bin QC

dialvarezs commented Dec 3, 2025

View reviewed changes

Comment thread CHANGELOG.md Outdated

jfy133 and others added 4 commits December 3, 2025 15:50

Update CHANGELOG.md

2ad091e

Co-authored-by: Diego Alvarez S. <[email protected]>

Support assembly input + long reads

f5aecb6

Update changelog

68492ba

Merge pull request #956 from dialvarezs/fix-lr-assembly-input

df02889

Support long reads assemblers in assembly input

dialvarezs merged commit ccfb744 into main Dec 5, 2025
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Release: v5.3.0 Rainbow Rattlesnake #948

Release: v5.3.0 Rainbow Rattlesnake #948
dialvarezs merged 186 commits intomainfrom
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