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Allow ABACAS for multifasta #481

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@cduong11 cduong11 commented Mar 25, 2025 •
edited by anfarr
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Proposed fix #461

  • Splitting the reference multifasta into individual fasta files (seqkit_split)
  • Processing each segment separately through ABACAS
  • Merging the results back into a single multifasta output (seqkit_concat)

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/viralrecon 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>).
  • 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).

@chaudb1998
splitting the reference multifasta into individual fasta files, proce…
fb35a1d 
…ssing each segment separately through ABACAS, merging the results back into a single multifasta output
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github-actions bot commented Mar 25, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 203542c

+| ✅ 203 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  48 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-viralrecon_logo_dark.png">\n <img alt="nf-core/viralrecon" src="docs/images/nf-core-viralrecon_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/viralrecon 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 1. Read QC (FastQC)2. 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/viralrecon \\\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/viralrecon was originally written by Patel H, Varona S and Monzon S.\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 #viralrecon 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/viralrecon 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 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 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 base.config: Check the defaults for all processes
  • system_exit - System.exit in nanopore.nf: System.exit(1) [line 246]
  • local_component_structure - rename_fasta_header.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_nanopore.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_mosdepth_regions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - snpeff_ann.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_blastn.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - prepare_primer_fasta.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_bed_mask.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - asciigenome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - plot_base_density.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - snpsift_extractfields.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - collapse_primers.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - make_variants_long_table.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - kraken2_build.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - snpeff_build.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc_illumina.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - ivar_variants_to_vcf.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - assembly_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - bam_trim_primers_ivar.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - consensus_bcftools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fastq_trim_fastp_fastqc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - vcf_bgzip_tabix_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - consensus_ivar.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - assembly_spades.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome_illumina.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variants_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - assembly_unicycler.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - snpeff_snpsift.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - consensus_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variants_bcftools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - abacas_multifasta.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variants_long_table.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - additional_annotation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - assembly_minia.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - vcf_tabix_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - filter_bam_samtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome_nanopore.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - variants_ivar.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-28 15:00:43

@cduong11 cduong11 requested a review from svarona March 25, 2025 09:53
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svarona commented Mar 25, 2025

Maybe we should add a CI test for that part of the code? Because as all the test-data is for SARS-CoV-2 which is not multifasta, it will never enter the CI tests.

Joon-Klaps
Joon-Klaps reviewed Mar 26, 2025
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Think we can simplify a couple of things

Joon-Klaps
Joon-Klaps reviewed Mar 28, 2025
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We're almost there :D

@cduong11
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Thank you so much @Joon-Klaps. I've edited as your suggestions.

Joon-Klaps
Joon-Klaps approved these changes Mar 28, 2025
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LGTM!

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@Joon-Klaps Joon-Klaps Joon-Klaps approved these changes

@svarona svarona Awaiting requested review from svarona

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@cduong11 @svarona @Joon-Klaps @chaudb1998