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Important! Template update for nf-core/tools v3.1.0 #10

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Important! Template update for nf-core/tools v3.1.0 #10

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Version 3.1.0 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.1.0 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.1.0 release page.

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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4b51a58

+| ✅ 188 tests passed       |+
!| ❗  43 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-tbanalyzer_logo_dark.png">\n <img alt="nf-core/tbanalyzer" src="docs/images/nf-core-tbanalyzer_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/tbanalyzer 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 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 Fill in short bullet-pointed list of the default steps in the pipeline \n\n1. Read QC (FastQC)\n2. Present QC for raw reads (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\nsamplesheet.csv:\n\ncsv\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 update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/tbanalyzer \\\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/tbanalyzer was originally written by @abhi18av.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n 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.\n\nFor further information or help, don't hesitate to get in touch on the Slack #tbanalyzer channel (you can join with this invite).\n\n## Citations\n\n 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/tbanalyzer for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n 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 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: Specify your pipeline's command line flags
  • 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • 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 README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in gatk4.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
  • pipeline_todos - TODO string in gatk4.nf: A module file SHOULD only define input and output files as command-line parameters.
  • pipeline_todos - TODO string in gatk4.nf: Software that can be piped together SHOULD be added to separate module files
  • pipeline_todos - TODO string in gatk4.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
  • pipeline_todos - TODO string in gatk4.nf: List required Conda package(s).
  • pipeline_todos - TODO string in gatk4.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
  • pipeline_todos - TODO string in gatk4.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
  • pipeline_todos - TODO string in gatk4.nf: Where applicable please provide/convert compressed files as input/output
  • pipeline_todos - TODO string in gatk4.nf: Named file extensions MUST be emitted for ALL output channels
  • pipeline_todos - TODO string in gatk4.nf: List additional required output channels/values here
  • pipeline_todos - TODO string in gatk4.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
  • pipeline_todos - TODO string in gatk4.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
  • pipeline_todos - TODO string in gatk4.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
  • pipeline_todos - TODO string in gatk4.nf: Please replace the example samtools command below with your module's command
  • pipeline_todos - TODO string in gatk4.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
  • pipeline_todos - TODO string in gatk4.nf: A stub section should mimic the execution of the original module as best as possible
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.0
  • Run at 2024-12-12 11:26:16

@nf-core-bot
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Version 3.1.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #11

Please use #11 to merge in the new changes from the nf-core template as soon as possible.

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