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Fix review comments #108

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Fix review comments #108

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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/magmap 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).
  • 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).

These were the last things that I needed to fix from James' review. After this PR and the #89 we can ask for a new round of review.

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github-actions bot commented Mar 7, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ba7c2a2

+| ✅ 217 tests passed       |+
!| ❗  20 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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: If you use nf-core/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

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

    GitHub 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/magmap is a bioinformatics best-practice analysis pipeline for mapping reads to a (large) collections of genomes.\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\nnf-core/magmap-metro-map\n\n1. Read QC (FastQC)\n2. Present QC for raw reads (MultiQC)\n3. Quality trimming and adapters removal for raw reads (Trim Galore!)\n4. Filter reads with BBduk\n5. Select reference genomes based on k-mer signatures in reads with sourmash\n6. Quantification of genes identified in selected reference genomes:\n 1. generate index of assembly (BBmap index)\n 2. Mapping cleaned reads to the assembly for quantification (BBmap)\n 3. Get raw counts per each gene present in the genomes (Featurecounts) -> TSV table with collected featurecounts output\n7. Summary statistics table. Collect_stats.R\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\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\nCONTROL_REP2,AEG588A1_S2_L002_R1_001.fastq.gz,AEG588A1_S2_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nAnd, if you want to map to a set of your own genomes, a genome information file looking like this:\n\ngenomeinfo.csv:\n\ncsv\naccno,genome_fna,genome_gff\ngenome1,path/to/fna.gz,path/to/gff.gz\ngenome2,path/to/fna.gz,path/to/gff.gz\ngenome3,path/to/fna.gz,path/to/gff.gz\n\n\nEach row represents a genome file with or without the paired gff\n\nNow, you can run the pipeline using:\n\nbash\nnextflow run nf-core/magmap --input samplesheet.csv --genomeinfo genomeinfo.csv --outdir <OUTDIR> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>\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/magmap was originally written by Danilo Di Leo @danilodileo, Emelie Nilsson @emnillson and Daniel Lundin @erikrikardaniel.\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 #magmap 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/magmap for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX 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",
  • local_component_structure - prokkagff2tsv.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - check_duplicates.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - genomeindex.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - create_accno_list.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - cat_many.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - filter_genomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - rename_contigs.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - collect_stats.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - collectgenomes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - collect_featurecounts.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - create_bbmap_index.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - concatenate_gff.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fastqc_trimgalore.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - sourmash.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - metadata.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-07 06:23:50

Danilo Di Leo added 2 commits March 7, 2025 07:20
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@erikrikarddaniel erikrikarddaniel Awaiting requested review from erikrikarddaniel

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