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Merge pull request #1005 from nf-core/dev
Release 5.4.2
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‎.nf-core.yml‎

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name: mag
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org: nf-core
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outdir: .
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version: 5.4.1
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version: 5.4.2

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## 5.4.2 Yellow Frog patch [2026-03-31]
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### `Added`
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- [#1006](https://github.com/nf-core/mag/pull/1006) - Add citations and references texts in the `utils_nfcore_mag_pipeline` subworkflow (by @dialvarezs)
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### `Changed`
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- [#1000](https://github.com/nf-core/mag/pull/1000) - Update GUNC modules and enable the tool in tests (by @dialvarezs)
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- [#1004](https://github.com/nf-core/mag/pull/1004) - Replace `collectFile` with `qsv/cat` on GUNC summary merging (by @dialvarezs)
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### `Fixed`
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- [#1001](https://github.com/nf-core/mag/pull/1001) - Include all binners in parameter validation for running DASTool (by @dialvarezs)
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- [#1002](https://github.com/nf-core/mag/pull/1002) - Fix BUSCO publish dir to prevent filename collision (by @dialvarezs)
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- [#1002](https://github.com/nf-core/mag/pull/1002) - Avoid whole-batch BUSCO failure when classification fails for a single bin. (by @dialvarezs)
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### `Dependencies`
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| Tool | Previous version | New version |
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| ---- | ---------------- | ----------- |
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| GUNC | 1.0.6 | 1.1.0 |
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## 5.4.1 - Yellow Frog patch [2026-03-13]
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### `Changed`
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### `Fixed`
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- [#974](https://github.com/nf-core/mag/pull/974) - Re-add accidently removed functionality for using metaSPAdes contigs downstream rather than scaffolds (reported by @Pranjal-Bioinfo, fix by @jfy133)
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- [#979](https://github.com/nf-core/mag/pull/979) - Re-add accidently removed functionality for using metaSPAdes contigs downstream rather than scaffolds (reported by @Pranjal-Bioinfo, fix by @jfy133)
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- [#984](https://github.com/nf-core/mag/pull/984) - Fix docs regarding usage of Bin QC tool scores when filtering bins for post-processing (by @dialvarezs, @claude)
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- [#987](https://github.com/nf-core/mag/pull/987) - Fix several documentation issues (by @dialvarezs)
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- [#988](https://github.com/nf-core/mag/pull/988) - Fix regarding validation of column `long_reads_platform` in the input samplesheet ([#985](https://github.com/nf-core/mag/issues/985) by @vinisalazar)

‎CITATIONS.md‎

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## Pipeline tools
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- [AdapterRemoval2](https://doi.org/10.1186/)
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- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)
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> Schubert, M., Lindgreen, S., and Orlando, L. 2016. "AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging." BMC Research Notes 9 (February): 88. doi: 10.1186/s13104-016-1900-2
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> Danecek, Petr, et al. "Twelve years of SAMtools and BCFtools." Gigascience 10.2 (2021): giab008. doi: 10.1093/gigascience/giab008
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- [Bowtie2](https:/dx.doi.org/10.1038/nmeth.1923)
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- [Bowtie2](https://doi.org/10.1038/nmeth.1923)
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> Langmead, B. and Salzberg, S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. doi: 10.1038/nmeth.1923.
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- [CheckM2](https://doi.org/10.1038/s41592-023-01940-w)
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> Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: https://doi.org/10.1038/s41592-023-01940-w
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> Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: 10.1038/s41592-023-01940-w
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- [Chopper](https://doi.org/10.1093/bioinformatics/bty149)
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> Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012
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- [geNomad](https://doi.org/10.1101/2023.03.05.531206)
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- [geNomad](https://doi.org/10.1038/s41587-023-01953-y)
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> Camargo, A. P., et al. (2023). You can move, but you can’t hide: identification of mobile genetic elements with geNomad. bioRxiv preprint. doi: 10.1101/2023.03.05.531206
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> Camargo, A. P., et al. (2023). Identification of mobile genetic elements with geNomad. Nature Biotechnology 42, 1303–1312. doi: 10.1038/s41587-023-01953-y
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- [GTDB-Tk](https://doi.org/10.1093/bioinformatics/btz848)
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- [BIgMAG](https://doi.org/10.12688/f1000research.152290.2)
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> Yepes-García, J., Falquet, L. (2024). Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG. F1000Research 13:640. doi.org/10.12688/f1000research.152290.2
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> Yepes-García, J., Falquet, L. (2024). Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG. F1000Research 13:640. doi: 10.12688/f1000research.152290.2
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- [MaxBin2](https://doi.org/10.1093/bioinformatics/btv638)
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- [MetaEuk](https://doi.org/10.1186/s40168-020-00808-x)
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> Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020). 10.1186/s40168-020-00808-x
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> Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020). doi: 10.1186/s40168-020-00808-x
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- [metaMDBG](https://doi.org/10.1038/s41587-023-01983-6)
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> Benoit, G., Raguideau, S., James, R. et al. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol 42, 1378–1383 (2024). doi:10.1038/s41587-023-01983-6
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> Benoit, G., Raguideau, S., James, R. et al. High-quality metagenome assembly from long accurate reads with metaMDBG. Nat Biotechnol 42, 1378–1383 (2024). doi: 10.1038/s41587-023-01983-6
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- [minimap2](https://doi.org/10.1093/bioinformatics/bty191)
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> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics , 34(18), 3094–3100. doi: 10.1093/bioinformatics/bty191
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- [MMseqs2](https://www.nature.com/articles/nbt.3988)
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> Steinegger, M., Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35, 1026–1028 (2017).10.1038/nbt.3988
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> Steinegger, M., Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35, 1026–1028 (2017). doi: 10.1038/nbt.3988
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- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
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> Karlicki, M., Antonowicz, S., Karnkowska, A., 2022. Tiara: deep learning-based classification system for eukaryotic sequences. Bioinformatics 38, 344–350. doi: 10.1093/bioinformatics/btab672
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- [Trimmomatic](https://doi.org/10.1093/bioinformatics/btu170)
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> Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. doi: 10.1093/bioinformatics/btu170
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## Data
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- [Full-size test data](https://doi.org/10.1038/s41587-019-0191-2)

‎assets/methods_description_template.yml‎

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section_name: "nf-core/mag Methods Description"
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section_href: "https://github.com/nf-core/mag"
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plot_type: "html"
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## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>
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<p>Data was processed using nf-core/mag v${workflow.manifest.version} (${doi_text}; <a href="https://doi.org/10.1093/nargab/lqac007">Krakau <em>et al.</em>, 2022</a>) of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>

‎assets/multiqc_config.yml‎

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/5.4.1" 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/5.4.1/docs/output" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/5.4.2" 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/5.4.2/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-mag-methods-description":
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order: -1000

‎conf/base.config‎

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withName: CHECKM2_PREDICT {
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errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
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}
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withName: 'CONCAT_BUSCO_TSV|CONCAT_CHECKM_TSV|CONCAT_CHECKM2_TSV|CONCAT_GUNC_TSV|CONCAT_GUNC_CHECKM_TSV' {
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cpus = 1
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memory = { 1.GB * task.attempt }
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}
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}

‎conf/modules.config‎

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withName: BUSCO_BUSCO {
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tag = { "${meta.assembler}-${meta.binner}-${meta.id}" }
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ext.args = [
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params.busco_db ? '--offline' : ''
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].join(' ').trim()
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tag = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
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ext.args = params.busco_db ? '--offline' : ''
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publishDir = [
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path: { "${params.outdir}/GenomeBinning/QC/BUSCO/${meta.assembler}-${meta.binner}-${meta.id}" },
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path: { "${params.outdir}/GenomeBinning/QC/BUSCO/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
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withName: 'CONCAT_BUSCO_TSV|CONCAT_CHECKM_TSV|CONCAT_CHECKM2_TSV' {
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withName: 'CONCAT_BUSCO_TSV|CONCAT_CHECKM_TSV|CONCAT_CHECKM2_TSV|CONCAT_GUNC_TSV|CONCAT_GUNC_CHECKM_TSV' {
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path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/" },
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path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/" },
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‎conf/test_assembly_input.config‎

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// TODO: enable when we have a suitable way to run a small test
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gunc_db = params.pipelines_testdata_base_path + 'mag/databases/gunc/gunc-mock.dmnd'
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‎docs/output.md‎

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<details markdown="1">
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<summary>Output files</summary>
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- `GenomeBinning/QC/BUSCO/[assembler]-[binner]-[sample/group]/`
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- `GenomeBinning/QC/BUSCO/[assembler]-[binner]-[domain]-[refinement]-[sample/group]/`
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- `[sample/group]-[lineage]-busco.batch_summary.txt`: Summary table of the BUSCO results for the bins in the sample.
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- `short_summary.generic.[lineage].[assembler]-[bin].{txt,json}`: A detailed BUSCO summary for each bin, available in both plain text and JSON format.
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- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[fasta input file name]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
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- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
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- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[checkm input file name]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
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- `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
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</details>
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‎main.nf‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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GENOME PARAMETER VALUES
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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*/
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// TODO nf-core: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
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// This is an example of how to use getGenomeAttribute() to fetch parameters
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// from igenomes.config using `--genome`
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// params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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NAMED WORKFLOWS FOR PIPELINE

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