diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index d4ade4cb..7e1e10b6 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/taxprofiler - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about + how to interpret these results, please see the documentation. report_section_order: "nf-core-taxprofiler-methods-description": order: -1000 @@ -60,23 +61,23 @@ custom_logo_url: https://nf-co.re/taxprofiler custom_logo_title: "nf-core/taxprofiler" run_modules: - - fastqc - - adapterremoval - - fastp - - nonpareil - - bbduk - - prinseqplusplus - - porechop - - filtlong - - nanoq - - bowtie2 - - samtools - - kraken - - kaiju - - diamond - - malt - - motus - - custom_content +- fastqc +- adapterremoval +- fastp +- nonpareil +- bbduk +- prinseqplusplus +- porechop +- filtlong +- nanoq +- bowtie2 +- samtools +- kraken +- kaiju +- diamond +- malt +- motus +- custom_content sp: diamond: @@ -92,67 +93,81 @@ sp: contents_re: " " top_modules: - - "fastqc": - name: "FastQC / Falco (pre-Trimming)" - path_filters: - - "*raw*" - path_filters_exclude: - - "*processed*" - extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." - - "fastqc": - name: "FastQC / Falco (post-Trimming)" - path_filters: - - "*processed*" - path_filters_exclude: - - "*raw*" - extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." - - nonpareil - - "porechop": - name: "Porechop" - anchor: "porechop" - target: "Porechop" - path_filters: - - "*porechop.log" - extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated." - - "porechop": - name: "Porechop_ABI" - anchor: "porechop_abi" - target: "Porechop_ABI" - doi: "10.1093/bioadv/vbac085" - info: "find and remove adapters from Oxford Nanopore reads." - path_filters: - - "*porechop_abi.log" - extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop_abi did not detect any adapters and therefore no statistics generated." - - "bowtie2": - name: "bowtie2" - - "samtools": - name: "Samtools Stats" - - "kraken": - name: "Kraken" - path_filters: - - "*.kraken2.kraken2.report.txt" - - "kraken": - name: "Bracken" - anchor: "bracken" - target: "Bracken" - doi: "10.7717/peerj-cs.104" - info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree." - extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC." - path_filters: - - "*.bracken.kraken2.report.txt" - - "kraken": - name: "Centrifuge" - anchor: "centrifuge" - target: "Centrifuge" - doi: "10.1101/gr.210641.116" - info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title" - extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above." - path_filters: - - "*.centrifuge.txt" - - "malt": - name: "MALT" - - "kaiju": - name: "Kaiju" +- "fastqc": + name: "FastQC / Falco (pre-Trimming)" + path_filters: + - "*raw*" + path_filters_exclude: + - "*processed*" + extra: "If used in this run, Falco is a drop-in replacement for FastQC producing + the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." +- "fastqc": + name: "FastQC / Falco (post-Trimming)" + path_filters: + - "*processed*" + path_filters_exclude: + - "*raw*" + extra: "If used in this run, Falco is a drop-in replacement for FastQC producing + the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." +- nonpareil +- "porechop": + name: "Porechop" + anchor: "porechop" + target: "Porechop" + path_filters: + - "*porechop.log" + extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' + this means that porechop did not detect any adapters and therefore no statistics + generated." +- "porechop": + name: "Porechop_ABI" + anchor: "porechop_abi" + target: "Porechop_ABI" + doi: "10.1093/bioadv/vbac085" + info: "find and remove adapters from Oxford Nanopore reads." + path_filters: + - "*porechop_abi.log" + extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' + this means that porechop_abi did not detect any adapters and therefore no statistics + generated." +- "bowtie2": + name: "bowtie2" +- "samtools": + name: "Samtools Stats" +- "kraken": + name: "Kraken" + path_filters: + - "*.kraken2.kraken2.report.txt" +- "kraken": + name: "Bracken" + anchor: "bracken" + target: "Bracken" + doi: "10.7717/peerj-cs.104" + info: "Estimates species abundances in metagenomics samples by probabilistically + re-distributing reads in the taxonomic tree." + extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing + the same output format as Kraken. Abundance information is currently not supported + in MultiQC." + path_filters: + - "*.bracken.kraken2.report.txt" +- "kraken": + name: "Centrifuge" + anchor: "centrifuge" + target: "Centrifuge" + doi: "10.1101/gr.210641.116" + info: "is a very rapid and memory-efficient system for the classification of DNA + sequences from microbial samples. The system uses a novel indexing scheme based + on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. + Note: Figure title" + extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output + format as Kraken. If activated, see the actual Kraken2 results in the section + above." + path_filters: + - "*.centrifuge.txt" +- "malt": + name: "MALT" +- "kaiju": + name: "Kaiju" # It is not possible to set placement for custom kraken # and centrifuge columns. @@ -264,29 +279,29 @@ table_columns_placement: table_columns_visible: FastQC / Falco (pre-Trimming): - total_sequences: True - avg_sequence_length: True - percent_duplicates: True - percent_gc: True - percent_fails: False + total_sequences: true + avg_sequence_length: true + percent_duplicates: true + percent_gc: true + percent_fails: false FastQC / Falco (post-Trimming): - total_sequences: True - avg_sequence_length: True - percent_duplicates: False - percent_gc: False - percent_fails: False + total_sequences: true + avg_sequence_length: true + percent_duplicates: false + percent_gc: false + percent_fails: false Adapter Removal: - aligned_total: True - percent_aligned: True - percent_collapsed: True - percent_discarded: False + aligned_total: true + percent_aligned: true + percent_collapsed: true + percent_discarded: false fastp: - pct_adapter: True - pct_surviving: True - pct_duplication: False - after_filtering_gc_content: False - after_filtering_q30_rate: False - after_filtering_q30_bases: False + pct_adapter: true + pct_surviving: true + pct_duplication: false + after_filtering_gc_content: false + after_filtering_q30_rate: false + after_filtering_q30_bases: false nonpareil: nonpareil_R: false nonpareil_LR: false @@ -294,51 +309,51 @@ table_columns_visible: nonpareil_C: true nonpareil_diversity: true porechop: - Input reads: False + Input reads: false Start Trimmed: - Start Trimmed Percent: True - End Trimmed: False - End Trimmed Percent: True - Middle Split: False - Middle Split Percent: True + Start Trimmed Percent: true + End Trimmed: false + End Trimmed Percent: true + Middle Split: false + Middle Split Percent: true porechop_abi: - Input reads: False + Input reads: false Start Trimmed: - Start Trimmed Percent: True - End Trimmed: False - End Trimmed Percent: True - Middle Split: False - Middle Split Percent: True + Start Trimmed Percent: true + End Trimmed: false + End Trimmed Percent: true + Middle Split: false + Middle Split Percent: true Filtlong: - Target bases: True + Target bases: true nanoq: - ReadN50: True - Reads: True + ReadN50: true + Reads: true BBDuk: - Input reads: False - Total Removed bases Percent: False - Total Removed bases: False - Total Removed reads percent: True - Total Removed reads: False + Input reads: false + Total Removed bases Percent: false + Total Removed bases: false + Total Removed reads percent: true + Total Removed reads: false "PRINSEQ++": - prinseqplusplus_total: True + prinseqplusplus_total: true bowtie2: - overall_alignment_rate: True + overall_alignment_rate: true Samtools Stats: - raw_total_sequences: True - reads_mapped: True - reads_mapped_percent: True - reads_properly_paired_percent: False - non-primary_alignments: False - reads_MQ0_percent: False - error_rate: False - Kraken: False - Bracken: False - Centrifuge: False - DIAMOND: False - Kaiju: False - MALT: False - motus: False + raw_total_sequences: true + reads_mapped: true + reads_mapped_percent: true + reads_properly_paired_percent: false + non-primary_alignments: false + reads_MQ0_percent: false + error_rate: false + Kraken: false + Bracken: false + Centrifuge: false + DIAMOND: false + Kaiju: false + MALT: false + motus: false table_columns_name: FastQC / Falco (pre-Trimming): @@ -359,18 +374,19 @@ table_columns_name: reads_mapped_percent: "% Mapped Reads" extra_fn_clean_exts: - - "kraken2.report.txt" - - ".txt" - - ".settings" - - ".bbduk" - - ".unmapped" - - "_filtered" - - "porechop" - - "porechop_abi" - - "_processed" - - ".diamond" - - type: remove - pattern: "_falco" +- "kraken2.report.txt" +- ".txt" +- ".settings" +- ".bbduk" +- ".unmapped" +- "_filtered" +- "porechop" +- "porechop_abi" +- "_processed" +- ".diamond" +- type: remove + pattern: "_falco" section_comments: - general_stats: "By default, all read count columns are displayed as millions (M) of reads." + general_stats: "By default, all read count columns are displayed as millions (M) + of reads." diff --git a/nextflow.config b/nextflow.config index 823fbf1b..125cd76d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -420,7 +420,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '1.3.0.dev' + version = '1.2.2' doi = '10.1101/2023.10.20.563221' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index edab4b1d..d5053bf0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-12T11:24:40+00:00", - "description": "

\n \n \n \"nf-core/taxprofiler\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\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/taxprofiler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![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/taxprofiler** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\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\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/taxprofiler \\\n -profile \\\n --input samplesheet.csv \\\n --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/taxprofiler/usage) and the [parameter documentation](https://nf-co.re/taxprofiler/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/taxprofiler/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/taxprofiler/output).\n\n## Credits\n\nnf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#taxprofiler` channel](https://nfcore.slack.com/channels/taxprofiler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\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", + "creativeWorkStatus": "Stable", + "datePublished": "2024-12-19T13:16:45+00:00", + "description": "

\n \n \n \"nf-core/taxprofiler\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/taxprofiler/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/taxprofiler/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/taxprofiler/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/taxprofiler/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7728364-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7728364)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\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/taxprofiler)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23taxprofiler-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/taxprofiler)[![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[![Cite Preprint](https://img.shields.io/badge/Cite%20Us!-Cite%20Preprint-orange)](https://doi.org/10.1101/2023.10.20.563221)\n\n## Introduction\n\n**nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases.\n\n## Pipeline summary\n\n![](docs/images/taxprofiler_tube.png)\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) or [`falco`](https://github.com/smithlabcode/falco) as an alternative option)\n2. Performs optional read pre-processing\n - Adapter clipping and merging (short-read: [fastp](https://github.com/OpenGene/fastp), [AdapterRemoval2](https://github.com/MikkelSchubert/adapterremoval); long-read: [porechop](https://github.com/rrwick/Porechop), [Porechop_ABI](https://github.com/bonsai-team/Porechop_ABI))\n - Low complexity and quality filtering (short-read: [bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus); long-read: [Filtlong](https://github.com/rrwick/Filtlong)), [Nanoq](https://github.com/esteinig/nanoq)\n - Host-read removal (short-read: [BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/); long-read: [Minimap2](https://github.com/lh3/minimap2))\n - Run merging\n3. Supports statistics metagenome coverage estimation ([Nonpareil](https://nonpareil.readthedocs.io/en/latest/)) and for host-read removal ([Samtools](http://www.htslib.org/))\n4. Performs taxonomic classification and/or profiling using one or more of:\n - [Kraken2](https://ccb.jhu.edu/software/kraken2/)\n - [MetaPhlAn](https://huttenhower.sph.harvard.edu/metaphlan/)\n - [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/)\n - [DIAMOND](https://github.com/bbuchfink/diamond)\n - [Centrifuge](https://ccb.jhu.edu/software/centrifuge/)\n - [Kaiju](https://kaiju.binf.ku.dk/)\n - [mOTUs](https://motu-tool.org/)\n - [KrakenUniq](https://github.com/fbreitwieser/krakenuniq)\n - [KMCP](https://github.com/shenwei356/kmcp)\n - [ganon](https://pirovc.github.io/ganon/)\n5. Perform optional post-processing with:\n - [bracken](https://ccb.jhu.edu/software/bracken/)\n6. Standardises output tables ([`Taxpasta`](https://taxpasta.readthedocs.io))\n7. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n8. Plotting Kraken2, Centrifuge, Kaiju and MALT results ([`Krona`](https://hpc.nih.gov/apps/kronatools.html))\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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,run_accession,instrument_platform,fastq_1,fastq_2,fasta\n2612,run1,ILLUMINA,2612_run1_R1.fq.gz,,\n2612,run2,ILLUMINA,2612_run2_R1.fq.gz,,\n2612,run3,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz,\n```\n\nEach row represents a fastq file (single-end), a pair of fastq files (paired end), or a fasta (with long reads).\n\nAdditionally, you will need a database sheet that looks as follows:\n\n`databases.csv`:\n\n```csv\ntool,db_name,db_params,db_path\nkraken2,db2,--quick,///kraken2/testdb-kraken2.tar.gz\nmetaphlan,db1,,///metaphlan/metaphlan_database/\n```\n\nThat includes directories or `.tar.gz` archives containing databases for the tools you wish to run the pipeline against.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/taxprofiler \\\n -profile \\\n --input samplesheet.csv \\\n --databases databases.csv \\\n --outdir \\\n --run_kraken2 --run_metaphlan\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/taxprofiler/usage) and the [parameter documentation](https://nf-co.re/taxprofiler/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/taxprofiler/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/taxprofiler/output).\n\n## Credits\n\nnf-core/taxprofiler was originally written by James A. Fellows Yates, Sofia Stamouli, Moritz E. Beber, Lili Andersson-Li, and the nf-core/taxprofiler team.\n\n### Team\n\n- [James A. Fellows Yates](https://github.com/jfy133)\n- [Sofia Stamouli](https://github.com/sofstam)\n- [Moritz E. Beber](https://github.com/Midnighter)\n- [Lili Andersson-Li](https://github.com/LilyAnderssonLee)\n\nWe thank the following people for their contributions to the development of this pipeline:\n\n- [Lauri Mesilaakso](https://github.com/ljmesi)\n- [Tanja Normark](https://github.com/talnor)\n- [Maxime Borry](https://github.com/maxibor)\n- [Thomas A. Christensen II](https://github.com/MillironX)\n- [Jianhong Ou](https://github.com/jianhong)\n- [Rafal Stepien](https://github.com/rafalstepien)\n- [Mahwash Jamy](https://github.com/mjamy)\n\n### Acknowledgments\n\nWe also are grateful for the feedback and comments from:\n\n- The general [nf-core/community](https://nf-co.re/community)\n\nAnd specifically to\n\n- [Alex H\u00fcbner](https://github.com/alexhbnr)\n\n\u2764\ufe0f also goes to [Zandra Fagern\u00e4s](https://github.com/ZandraFagernas) for the logo.\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 `#taxprofiler` channel](https://nfcore.slack.com/channels/taxprofiler) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/taxprofiler for your analysis, please cite it using the following doi: [10.1101/2023.10.20.563221](https://doi.org/10.1101/2023.10.20.563221).\n\n> Stamouli, S., Beber, M. E., Normark, T., Christensen II, T. A., Andersson-Li, L., Borry, M., Jamy, M., nf-core community, & Fellows Yates, J. A. (2023). nf-core/taxprofiler: Highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. In bioRxiv (p. 2023.10.20.563221). https://doi.org/10.1101/2023.10.20.563221\n\nFor the latest version of the code, cite the Zenodo doi: [10.5281/zenodo.7728364](https://doi.org/10.5281/zenodo.7728364)\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": [ { "@id": "main.nf" @@ -43,6 +43,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +102,7 @@ }, "mentions": [ { - "@id": "#b0b17d54-aec2-45a9-b037-baf14da78a78" + "@id": "#fcb90b4f-361a-4105-ba52-352fef2612cf" } ], "name": "nf-core/taxprofiler" @@ -121,14 +124,27 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "creator": [ { "@id": "#jfy133@gmail.com" + }, + { + "@id": "#jfy133@gmail.com" + }, + { + "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com" + }, + { + "@id": "https://orcid.org/0009-0006-0893-3771" } ], "dateCreated": "", - "dateModified": "2024-12-12T11:24:40Z", + "dateModified": "2024-12-19T14:16:45Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -145,16 +161,36 @@ "taxonomic-classification", "taxonomic-profiling" ], - "license": ["MIT"], - "name": ["nf-core/taxprofiler"], + "license": [ + "MIT" + ], + "maintainer": [ + { + "@id": "#jfy133@gmail.com" + }, + { + "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com" + }, + { + "@id": "https://orcid.org/0009-0006-0893-3771" + } + ], + "name": [ + "nf-core/taxprofiler" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/taxprofiler", "https://nf-co.re/taxprofiler/dev/"], - "version": ["1.3.0dev"] + "url": [ + "https://github.com/nf-core/taxprofiler", + "https://nf-co.re/taxprofiler/1.2.2/" + ], + "version": [ + "1.2.2" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -169,11 +205,11 @@ "version": "!>=24.04.2" }, { - "@id": "#b0b17d54-aec2-45a9-b037-baf14da78a78", + "@id": "#fcb90b4f-361a-4105-ba52-352fef2612cf", "@type": "TestSuite", "instance": [ { - "@id": "#2a4bf297-5ebe-481c-84e1-ef897f23e5c9" + "@id": "#30333f3e-d4b1-436d-b081-9abb665f69b7" } ], "mainEntity": { @@ -182,7 +218,7 @@ "name": "Test suite for nf-core/taxprofiler" }, { - "@id": "#2a4bf297-5ebe-481c-84e1-ef897f23e5c9", + "@id": "#30333f3e-d4b1-436d-b081-9abb665f69b7", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/taxprofiler", "resource": "repos/nf-core/taxprofiler/actions/workflows/ci.yml", @@ -224,6 +260,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -314,7 +355,19 @@ "@id": "#jfy133@gmail.com", "@type": "Person", "email": "jfy133@gmail.com", - "name": "James Fellows Yates" + "name": "James A. Fellows Yates" + }, + { + "@id": "#64467552+LilyAnderssonLee@users.noreply.github.com", + "@type": "Person", + "email": "64467552+LilyAnderssonLee@users.noreply.github.com", + "name": "Lili Andersson-Li" + }, + { + "@id": "https://orcid.org/0009-0006-0893-3771", + "@type": "Person", + "email": "91951607+sofstam@users.noreply.github.com", + "name": "Sofia Stamouli" } ] -} +} \ No newline at end of file