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Bump version for 2.3.0 release #184

Merged
merged 3 commits into from
Dec 23, 2024
Merged

Bump version for 2.3.0 release #184

merged 3 commits into from
Dec 23, 2024

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edmundmiller
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  • chore: Add new contributors section
  • chore: Capture Template updates
  • chore: Bump version to 2.3.0

@edmundmiller edmundmiller self-assigned this Dec 22, 2024
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github-actions bot commented Dec 22, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d20685a

+| ✅ 220 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.3.0
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-nascent_logo_dark.png">\n <img alt="nf-core/nascent" src="docs/images/nf-core-nascent_logo_light.png">\n \n

    \n\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/nascent is a bioinformatics best-practice analysis pipeline for nascent transcript (NT) and Transcriptional Start Site (TSS) assays.\n\nThe pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!\n\nOn 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.\n\n## Pipeline summary\n\n1. Read QC (FastQC)\n2. Adapter and quality trimming (fastp)\n3. Alignment\n 1. bwa\n 2. bwamem2\n 3. DRAGMAP\n4. Sort and index alignments (SAMtools)\n5. UMI-based deduplication (UMI-tools)\n6. Duplicate read marking (picard MarkDuplicates)\n7. Quality Control\n 1. RSeQC - Various RNA-seq QC metrics\n 2. Preseq - Estimation of library complexity\n 3. BBMap - Analyzes the sequencing coverage\n8. Coverage Graphs\n 1. Create bedGraph coverage files (BEDTools\n 2. Create bigWig coverage files (deeptools)\n9. Transcript identification\n 1. HOMER\n 2. GroHMM\n 3. PINTS\n10. Quantification of Genes and Nascent Transcripts (featureCounts)\n11. Aggregate report describing results and QC from the whole pipeline (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.\n\n 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\ncsv title=\"samplesheet.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\nbash\nnextflow run nf-core/nascent \\\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.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/nascent was originally written by Ignacio Tripodi (@ignaciot) and Margaret Gruca (@magruca).\n\nThe pipeline was re-written in Nextflow DSL2 by Edmund Miller (@edmundmiller) and Sruthi Suresh (@sruthipsuresh) from The Functional Genomics Laboratory at The Univeristy of Texas at Dallas\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- @apeltzer\n- @ewels\n- @drpatelh\n- @pditommaso\n- @FriederikeHanssen\n- Tae Hoon Kim\n- @easterwoods\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #nascent channel (you can join with this invite).\n\n## Citations\n\nIf you use nf-core/nascent for your analysis, please cite it using the following doi: 10.5281/zenodo.7245273\n\nAn extensive list of references for the tools used by the pipeline can be found in the 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.\n",
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2024-12-22 18:28:48

@edmundmiller edmundmiller added this to the 2.3.0 milestone Dec 22, 2024
@edmundmiller edmundmiller mentioned this pull request Dec 23, 2024
Open
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@edmundmiller edmundmiller merged commit 7d33c65 into dev Dec 23, 2024
14 checks passed
@edmundmiller edmundmiller deleted the 2.3.0-release branch December 23, 2024 13:47
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@mashehu mashehu mashehu approved these changes

@sateeshperi sateeshperi sateeshperi approved these changes

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