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nf-core · Dec 19, 2024 · 9e46e4d · 9e46e4d
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diff --git a/.nf-core.yml b/.nf-core.yml
@@ -16,4 +16,4 @@ template:
   name: mag
   org: nf-core
   outdir: .
-  version: dev
+  version: 3.3.1dev
diff --git a/nextflow.config b/nextflow.config
@@ -455,7 +455,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = 'dev'
+    version         = '3.3.1dev'
     doi             = '10.1093/nargab/lqac007'
 }
 

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -22,7 +22,7 @@
             "@id": "./",
             "@type": "Dataset",
             "creativeWorkStatus": "InProgress",
-            "datePublished": "2024-12-19T13:11:40+00:00",
+            "datePublished": "2024-12-19T13:13:43+00:00",
             "description": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/mag_logo_mascot_dark.png\">\n    <img alt=\"nf-core/mag\" src=\"docs/images/mag_logo_mascot_light.png\">\n  </picture>\n</h1>\n\n[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3589527-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3589527)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-orange)](https://doi.org/10.1093/nargab/lqac007)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/mag)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/mag** is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes.\n\n<p align=\"center\">\n    <img src=\"docs/images/mag_workflow.png\" alt=\"nf-core/mag workflow overview\" width=\"90%\">\n</p>\n\n## Pipeline summary\n\nBy default, the pipeline currently performs the following: it supports both short and long reads, quality trims the reads and adapters with [fastp](https://github.com/OpenGene/fastp) and [Porechop](https://github.com/rrwick/Porechop), and performs basic QC with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and merge multiple sequencing runs.\n\nThe pipeline then:\n\n- assigns taxonomy to reads using [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [Kraken2](https://github.com/DerrickWood/kraken2/wiki)\n- 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)\n- (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)\n- 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)\n- performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and 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/).\n- Performs ancient DNA validation and repair with [pyDamage](https://github.com/maxibor/pydamage) and [freebayes](https://github.com/freebayes/freebayes)\n- optionally refines bins with [DAS Tool](https://github.com/cmks/DAS_Tool)\n- assigns taxonomy to bins using [GTDB-Tk](https://github.com/Ecogenomics/GTDBTk) and/or [CAT](https://github.com/dutilh/CAT) and optionally identifies viruses in assemblies using [geNomad](https://github.com/apcamargo/genomad), or Eukaryotes with [Tiara](https://github.com/ibe-uw/tiara)\n\nFurthermore, the pipeline creates various reports in the results directory specified, including a [MultiQC](https://multiqc.info/) report summarizing some of the findings and software versions.\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n```bash\nnextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --outdir <OUTDIR>\n```\n\nor\n\n```bash\nnextflow run nf-core/mag -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR>\n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/mag/usage) and the [parameter documentation](https://nf-co.re/mag/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/mag/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/mag/output).\n\n### Group-wise co-assembly and co-abundance computation\n\nEach sample has an associated group ID (see [input specifications](https://nf-co.re/mag/usage#input_specifications)). This group information can be used for group-wise co-assembly with `MEGAHIT` or `SPAdes` and/or to compute co-abundances for the binning step with `MetaBAT2`. By default, group-wise co-assembly is disabled, while the computation of group-wise co-abundances is enabled. For more information about how this group information can be used see the documentation for the parameters [`--coassemble_group`](https://nf-co.re/mag/parameters#coassemble_group) and [`--binning_map_mode`](https://nf-co.re/mag/parameters#binning_map_mode).\n\nWhen group-wise co-assembly is enabled, `SPAdes` is run on accordingly pooled read files, since `metaSPAdes` does not yet allow the input of multiple samples or libraries. In contrast, `MEGAHIT` is run for each group while supplying lists of the individual readfiles.\n\n## Credits\n\nnf-core/mag was written by [Hadrien Gourl\u00e9](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0.\n\nOther code contributors include:\n\n- [Antonia Schuster](https://github.com/AntoniaSchuster)\n- [Alexander Ramos](https://github.com/alxndrdiaz)\n- [Carson Miller](https://github.com/CarsonJM)\n- [Daniel Lundin](https://github.com/erikrikarddaniel)\n- [Danielle Callan](https://github.com/d-callan)\n- [Gregory Sprenger](https://github.com/gregorysprenger)\n- [Jim Downie](https://github.com/prototaxites)\n- [Phil Palmer](https://github.com/PhilPalmer)\n- [@willros](https://github.com/willros)\n- [Adam Rosenbaum](https://github.com/muabnezor)\n- [Diego Alvarez](https://github.com/dialvarezs)\n\nLong read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Alexander Peltzer](https://github.com/apeltzer)\n- [Phil Ewels](https://github.com/ewels)\n- [Gisela Gabernet](https://github.com/ggabernet)\n- [Harshil Patel](https://github.com/drpatelh)\n- [Johannes Alneberg](https://github.com/alneberg)\n- [Maxime Garcia](https://github.com/MaxUlysse)\n- [Michael L Heuer](https://github.com/heuermh)\n- [Alex H\u00fcbner](https://github.com/alexhbnr)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#mag` channel](https://nfcore.slack.com/channels/mag) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/mag for your analysis, please cite the preprint as follows:\n\n> **nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning**\n>\n> Sabrina Krakau, Daniel Straub, Hadrien Gourl\u00e9, Gisela Gabernet, Sven Nahnsen.\n>\n> NAR Genom Bioinform. 2022 Feb 2;4(1):lqac007. doi: [10.1093/nargab/lqac007](https://doi.org/10.1093/nargab/lqac007).\n\nAdditionally you can cite the pipeline directly with the following doi: [10.5281/zenodo.3589527](https://doi.org/10.5281/zenodo.3589527)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n",
             "hasPart": [
                 {
@@ -105,7 +105,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#ba9e82b6-9e8c-418a-9330-f10eadfc36e9"
+                    "@id": "#69a630c2-4ecb-45c8-aa72-507b7379fdc9"
                 }
             ],
             "name": "nf-core/mag"
@@ -134,16 +134,16 @@
             ],
             "creator": [
                 {
-                    "@id": "#[email protected].com"
+                    "@id": "#jfy133@gmail.com"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0003-0603-7907"
+                    "@id": "#[email protected]"
                 },
                 {
-                    "@id": "#[email protected]"
+                    "@id": "https://orcid.org/0000-0003-0603-7907"
                 },
                 {
-                    "@id": "#68351153+CarsonJM@users.noreply.github.com"
+                    "@id": "#42973691+d4straub@users.noreply.github.com"
                 },
                 {
                     "@id": "https://orcid.org/0000-0001-9807-1082"
@@ -153,7 +153,7 @@
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             ],
             "dateCreated": "",
-            "dateModified": "2024-12-19T14:11:40Z",
+            "dateModified": "2024-12-19T14:13:43Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -172,13 +172,13 @@
             ],
             "maintainer": [
                 {
-                    "@id": "#[email protected].com"
+                    "@id": "#jfy133@gmail.com"
                 },
                 {
                     "@id": "https://orcid.org/0000-0003-0603-7907"
                 },
                 {
-                    "@id": "#jfy133@gmail.com"
+                    "@id": "#[email protected].com"
                 },
                 {
                     "@id": "https://orcid.org/0000-0001-9807-1082"
@@ -198,7 +198,7 @@
                 "https://nf-co.re/mag/dev/"
             ],
             "version": [
-                "dev"
+                "3.3.1dev"
             ]
         },
         {
@@ -214,11 +214,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#ba9e82b6-9e8c-418a-9330-f10eadfc36e9",
+            "@id": "#69a630c2-4ecb-45c8-aa72-507b7379fdc9",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#0bf3475f-69d5-4c2b-bade-d2359b2e46ce"
+                    "@id": "#9a41f8df-23bd-4f5e-be1a-719ffff430a4"
                 }
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             "mainEntity": {
@@ -227,7 +227,7 @@
             "name": "Test suite for nf-core/mag"
         },
         {
-            "@id": "#0bf3475f-69d5-4c2b-bade-d2359b2e46ce",
+            "@id": "#9a41f8df-23bd-4f5e-be1a-719ffff430a4",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/mag",
             "resource": "repos/nf-core/mag/actions/workflows/ci.yml",
@@ -365,18 +365,6 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "#[email protected]",
-            "@type": "Person",
-            "email": "[email protected]",
-            "name": "Daniel Straub"
-        },
-        {
-            "@id": "https://orcid.org/0000-0003-0603-7907",
-            "@type": "Person",
-            "email": "[email protected]",
-            "name": "Sabrina Krakau"
-        },
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             "@id": "#[email protected]",
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@@ -389,6 +377,18 @@
             "email": "[email protected]",
             "name": "Carson J Miller"
         },
+        {
+            "@id": "https://orcid.org/0000-0003-0603-7907",
+            "@type": "Person",
+            "email": "[email protected]",
+            "name": "Sabrina Krakau"
+        },
+        {
+            "@id": "#[email protected]",
+            "@type": "Person",
+            "email": "[email protected]",
+            "name": "Daniel Straub"
+        },
         {
             "@id": "https://orcid.org/0000-0001-9807-1082",
             "@type": "Person",