# nf-core/metatdenovo

#

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On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/metatdenovo/results). ## Usage ![nf-core/metatdenovo metro map](docs/images/metat-metromap.png) 1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) 2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) 3. Quality trimming and adapter removal for raw reads ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)) 4. Optional: Filter sequences with [`BBduk`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/) 5. Optional: Normalize the sequencing depth with [`BBnorm`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/) 6. Merge trimmed, pair-end reads ([`Seqtk`](https://github.com/lh3/seqtk)) 7. Choice of de novo assembly programs: 1. [`RNAspades`](https://cab.spbu.ru/software/rnaspades/) suggested for both prokaryote and eukaryote assembly 2. [`Megahit`](https://github.com/voutcn/megahit) suggested for both prokaryote and eukaryote assembly; requires less resources 8. Choice of orf caller: 1. [`TransDecoder`](https://github.com/TransDecoder/TransDecoder) suggested for eukaryotes; only ORFs 2. [`Prokka`](https://github.com/tseemann/prokka) suggested for prokaryotes; ORFs and other features plus functional annotation 3. [`Prodigal`](https://github.com/hyattpd/Prodigal) suggested for Prokaryotes; only ORFs 9. Quantification of genes identified in assemblies: 1. Generate index of assembly ([`BBmap index`](https://sourceforge.net/projects/bbmap/)) 2. Mapping cleaned reads to the assembly for quantification ([`BBmap`](https://sourceforge.net/projects/bbmap/)) 3. Get raw counts per each gene present in the assembly ([`Featurecounts`](http://subread.sourceforge.net)) -> TSV table with collected featurecounts output 10. Functional annotation: 1. [`Prokka`](https://github.com/tseemann/prokka) feature identification and annotation for prokaryotes 2. [`eggNOG-mapper`](https://github.com/eggnogdb/eggnog-mapper) 3. [`KofamScan`](https://github.com/takaram/kofam_scan) 4. [`HMMER`](https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch) search ORFs with a set of HMM profiles, and rank results 11. Taxonomic annotation: 1. [`EUKulele`](https://github.com/AlexanderLabWHOI/EUKulele) 2. [`Diamond`](https://github.com/bbuchfink/diamond) 12. Summary statistics. ## Usage > [!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. First, prepare a samplesheet with your input data that looks as follows: `samplesheet.csv`: ``` sample,fastq_1,fastq_2 sample1,./data/S1_R1_001.fastq.gz,./data/S1_R2_001.fastq.gz sample2,./data/S2_fw.fastq.gz,./data/S2_rv.fastq.gz sample3,./S4x.fastq.gz,./S4y.fastq.gz sample3,./a.fastq.gz,./b.fastq.gz ``` Each row represents a fastq file (single-end) or a pair of fastq files (paired-end). The fastq files need to end with `.fq` or `.fastq`, followed by `.gz` if gzipped. Read files from multiple rows with the same sample name will be concatenated and treated as a single sample. A mix of single-end and paired-end files is allowed, but do not mix single-end and paired-end for the same sample name. Now, you can run the pipeline using: ```bash nextflow run nf-core/metatdenovo \ -profile \ --input samplesheet.csv \ --outdir ``` > [!WARNING] > 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). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/metatdenovo/usage) and the [parameter documentation](https://nf-co.re/metatdenovo/parameters). ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/metatdenovo/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/metatdenovo/output). > [!NOTE] > Tables in the `summary_tables` directory under the output directory are made especially for further analysis in tools like R or Python. > Their formats are standardized and column names consistent between tables. ## Credits nf-core/metatdenovo was originally written by Danilo Di Leo (@danilodileo), Emelie Nilsson (@emnilsson) & Daniel Lundin (@erikrikarddaniel). ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). For further information or help, don't hesitate to get in touch on the [Slack `#metatdenovo` channel](https://nfcore.slack.com/channels/metatdenovo) (you can join with [this invite](https://nf-co.re/join/slack)). ## Citations If you use nf-core/metatdenovo for your analysis, please cite it using the following doi: [10.5281/zenodo.10666590](https://doi.org/10.5281/zenodo.10666590) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: > **The nf-core framework for community-curated bioinformatics pipelines.** > > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).

License
  MIT

## Contents

- ["nf-core/metatdenovo"]
- assets/
- conf/
- docs/
- docs/images/
- modules/
- modules/local/
- modules/nf-core/
- workflows/
- subworkflows/
- nextflow.config
- README.md
- nextflow_schema.json
- CHANGELOG.md
- LICENSE
- CODE_OF_CONDUCT.md
- CITATIONS.md
- modules.json
- docs/usage.md
- docs/output.md
- .nf-core.yml
- .pre-commit-config.yaml
- .prettierignore