|
22 | 22 | "@id": "./", |
23 | 23 | "@type": "Dataset", |
24 | 24 | "creativeWorkStatus": "InProgress", |
25 | | - "datePublished": "2025-05-23T09:44:35+00:00", |
26 | | - "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-denovotranscript_logo_dark.png\">\n <img alt=\"nf-core/denovotranscript\" src=\"docs/images/nf-core-denovotranscript_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml)\n[](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml)[](https://nf-co.re/denovotranscript/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/denovotranscript)\n\n[](https://nfcore.slack.com/channels/denovotranscript)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/denovotranscript** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. 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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/denovotranscript \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --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/denovotranscript/usage) and the [parameter documentation](https://nf-co.re/denovotranscript/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/denovotranscript/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/denovotranscript/output).\n\n## Credits\n\nnf-core/denovotranscript was originally written by Avani Bhojwani and Timothy Little.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\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 `#denovotranscript` channel](https://nfcore.slack.com/channels/denovotranscript) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/denovotranscript for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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", |
| 25 | + "datePublished": "2025-05-26T15:51:56+00:00", |
| 26 | + "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-denovotranscript_logo_dark.png\">\n <img alt=\"nf-core/denovotranscript\" src=\"docs/images/nf-core-denovotranscript_logo_light.png\">\n </picture>\n</h1>\n[](https://github.com/nf-core/denovotranscript/actions/workflows/ci.yml)\n[](https://github.com/nf-core/denovotranscript/actions/workflows/linting.yml)[](https://nf-co.re/denovotranscript/results)[](https://doi.org/10.5281/zenodo.13324371)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/denovotranscript)\n\n[](https://nfcore.slack.com/channels/denovotranscript)[](https://twitter.com/nf_core)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/denovotranscript** is a bioinformatics pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq. It takes a samplesheet and FASTQ files as input, perfoms quality control (QC), trimming, assembly, redundancy reduction, pseudoalignment, and quantification. It outputs a transcriptome assembly FASTA file, a transcript abundance TSV file, and a MultiQC report with assembly quality and read QC metrics.\n\n\n\n1. Read QC of raw reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Adapter and quality trimming ([`fastp`](https://github.com/OpenGene/fastp))\n3. Read QC of trimmed reads ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n4. Remove rRNA or mitochondrial DNA (optional) ([`SortMeRNA`](https://hpc.nih.gov/apps/sortmeRNA.html))\n5. Transcriptome assembly using any combination of the following:\n\n - [`Trinity`](https://github.com/trinityrnaseq/trinityrnaseq/wiki) with normalised reads (default=True)\n - [`Trinity`](https://github.com/trinityrnaseq/trinityrnaseq/wiki) with non-normalised reads\n - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) medium filtered transcripts outputted (default=True)\n - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) soft filtered transcripts outputted\n - [`rnaSPAdes`](https://ablab.github.io/spades/rna.html) hard filtered transcripts outputted\n\n6. Redundancy reduction with [`Evidential Gene tr2aacds`](http://arthropods.eugenes.org/EvidentialGene/). A transcript to gene mapping is produced from Evidential Gene's outputs using [`gawk`](https://www.gnu.org/software/gawk/).\n7. Assembly completeness QC ([`BUSCO`](https://busco.ezlab.org/))\n8. Other assembly quality metrics ([`rnaQUAST`](https://github.com/ablab/rnaquast))\n9. Transcriptome quality assessment with [`TransRate`](https://hibberdlab.com/transrate/), including the use of reads for assembly evaluation. This step is not performed if profile is set to `conda` or `mamba`.\n10. Pseudo-alignment and quantification ([`Salmon`](https://combine-lab.github.io/salmon/))\n11. HTML report for raw reads, trimmed reads, BUSCO, and Salmon ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a pair of fastq files (paired end).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/denovotranscript \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --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/denovotranscript/usage) and the [parameter documentation](https://nf-co.re/denovotranscript/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/denovotranscript/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/denovotranscript/output).\n\n## Credits\n\nnf-core/denovotranscript was written by Avani Bhojwani ([@avani-bhojwani](https://github.com/avani-bhojwani/)) and Timothy Little ([@timslittle](https://github.com/timslittle/)).\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 `#denovotranscript` channel](https://nfcore.slack.com/channels/denovotranscript) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/denovotranscript for your analysis, please cite it using the following doi: [10.5281/zenodo.13324371](https://doi.org/10.5281/zenodo.13324371)\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", |
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