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Added parameter hic_alphanumeric_sort #192

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Added parameter hic_alphanumeric_sort #192

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@GallVp GallVp commented Mar 12, 2025

PR checklist

  • Added parameter hic_alphanumeric_sort
  • 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
  • Make sure your code lints (nf-core pipelines 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).

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github-actions bot commented Mar 12, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f4a6272

+| ✅ 167 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗  32 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "# plant-food-research-open/assemblyqc\n\nGitHub Actions CI Status\nGitHub Actions Linting StatusCite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\n## Introduction\n\nplant-food-research-open/assemblyqc 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\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 plant-food-research-open/assemblyqc \\\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\n## Credits\n\nplant-food-research-open/assemblyqc was originally written by Usman Rashid, Ken Smith, Ross Crowhurst, Chen Wu, Marcus Davy.\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\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 plant-food-research-open/assemblyqc 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\nThis pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.\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",
  • local_component_structure - mummer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - hicqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - ncbi_fcs_gx_krona_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - matlock_bam2_juicer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - linearsynteny.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - assembly2bedpe.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - generatekaryotype.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2_krona_plot.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - dnadiff.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - colourbundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - runassemblyvisualizer.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - juicer_sort.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - hic2html.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - relabelfastalength.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - agp2assembly.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - bundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - circos.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - makeagpfromfasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - relabelbundlelinks.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filtersortfasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - createreport.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - assemblathon_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - splitbundlefile.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - ncbi_fcs_gx_screen_samples.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - ncbi_fcs_gx_setup_sample.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - getfastalength.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - ncbi_fcs_gx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fq2hic.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fasta_synteny.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fasta_kraken2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-assemblyqc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-assemblyqc_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: validation.help.beforeText
  • nextflow_config - Config variable ignored: validation.help.afterText
  • nextflow_config - Config variable ignored: validation.summary.beforeText
  • nextflow_config - Config variable ignored: validation.summary.afterText
  • files_unchanged - File does not exist: CODE_OF_CONDUCT.md
  • 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/CONTRIBUTING.md
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-assemblyqc_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-assemblyqc_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml
  • template_strings - template_strings
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-12 00:26:02

@GallVp
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GallVp commented Mar 12, 2025

For visibility, @ignacio3437, @SarahBailey1998, @christinawu2008

@GallVp GallVp added this to the 2.3.0 milestone Mar 12, 2025
@GallVp GallVp linked an issue Mar 12, 2025 that may be closed by this pull request
Make the alphanumeric FASTA sequence sorting in HiC map optional #188
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Make the alphanumeric FASTA sequence sorting in HiC map optional
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