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Dev => Master 2.3.0 #185

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@edmundmiller edmundmiller commented Dec 23, 2024 •
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Waiting for #184

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/nascent branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

edmundmiller and others added 30 commits March 20, 2024 12:10
@edmundmiller
build: Give up and use biocontainers
2c99fcc
@edmundmiller
style: Add \'s
1419c9e
@edmundmiller
fix(dreg_prep): Use task.cpus
cbcdf6e
@edmundmiller
refactor(dreg_prep): Use sort instead of sortBed
e6a297d 
https://bedtools.readthedocs.io/en/latest/content/tools/sort.html#optional-sorting-behavior
@edmundmiller
fix(dreg_prep): Make it a process low
b110704 
The only thing using more than one thread is samtools
@edmundmiller
feat: Start DREG_PREP Subworkflow
899ac94
@edmundmiller
build: nf-core subworkflows install fastq_align_star
43194a8
@edmundmiller
feat: Add STAR Alignment
7161b14
@edmundmiller
build: nf-core modules install star/genomegenerate
6d27d26
@edmundmiller
feat: Add basic STAR index generation
9916891
@edmundmiller
fix: Copy over config from rnaseq
df6c876
@edmundmiller
ci: Use detect-nf-test-changes
95187c4 
https://github.com/nf-core/phageannotator/blob/f9da24f4beb5775735a28d98327bd92755517a8a/.github/workflows/ci.yml
@edmundmiller
test: Use testsDir "."
749d703 
Not sure how that snuck back in there
@edmundmiller
test: Write basic STAR test
ca68e9b
@edmundmiller
fix: Make sure the gtf is unzipped
9940414
@edmundmiller
docs: Add info about the sample column concatinating group and replic…
3d4db1d 
…ate columns
@edmundmiller
refactor: Pass bais to transcript identification for PINTS
c49e9d7
@edmundmiller
feat: Bump CHM13 fasta
2aeb303
@edmundmiller
fix: Update CHM13
63f5074
@edmundmiller
chore: Update CHANGELOG
4bd6a11
@edmundmiller @maxulysse
build: Add params.human-pandgenomics_base
c47db7e 
Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>
@edmundmiller
Merge pull request #142 from nf-core/STAR
9561941 
Add STAR aligner
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 2.14.0
25f8d5d
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 2.14.1
5522aab
@edmundmiller
style: Try to fix linting
25d8803
@edmundmiller
build: Remove extra "groseq" workflow
0280009
@edmundmiller
chore: nf-core modules update
47ba2f4
@edmundmiller
fix: Catch up with module updates
64acae7
@edmundmiller
chore: nf-core modules update subworkflow
ed8510f
@edmundmiller
ci: Bump detect-nf-test-changes to 0.0.3
45455b6
edmundmiller and others added 18 commits December 20, 2024 06:50
@edmundmiller
test: Maybe this was causing some deterministic issue
6f6af11
@edmundmiller
test: Fix ignore samtools
6329b2c
@edmundmiller
test: That's why STAR is outputting samtools
3b9ee15
@edmundmiller
Merge pull request #182 from nf-core/nft-utils
bb5a3a8 
Adopt nft-utils
@edmundmiller
test(#57): Add uniqmap test
5b21392
@edmundmiller
chore: nf-core subworkflows update homer_groseq
96a9f4d
@edmundmiller
Merge pull request #177 from nf-core/homer-uniqmap
2d19d95 
test(#57): Add uniqmap test
@edmundmiller
chore: Fix config selectors
c0d2709
@edmundmiller
fix: Remove Transcriptome quant from STAR
723e873
@edmundmiller
Merge pull request #173 from nf-core/fix-config-selectors
7425043
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 3.1.0
bfcd97c
@nf-core-bot @edmundmiller
Template update for nf-core/tools version 3.1.1
7a4e356
@edmundmiller
chore: Fix pipeline => nascent
ba48eb2
@edmundmiller
style: First pass with lsp
e6b3ecd
@edmundmiller
Merge pull request #180 from nf-core/lsp-formatting
ae6518e 
Run lsp formatting
@edmundmiller
chore: Add new contributors section
1bda499
@edmundmiller
chore: Capture Template updates
0cb4601
@edmundmiller
chore: Bump version to 2.3.0
d20685a
@edmundmiller edmundmiller self-assigned this Dec 23, 2024
@edmundmiller edmundmiller added this to the 2.3.0 milestone Dec 23, 2024
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github-actions bot commented Dec 23, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7d9ce8a

+| ✅ 223 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 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 2024-12-29 04:09:25

@edmundmiller
Merge pull request #184 from nf-core/2.3.0-release
7d33c65 
Bump version for 2.3.0 release
@edmundmiller edmundmiller marked this pull request as ready for review December 23, 2024 13:47
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