RO-crate content appear in the nf-core lint warning if there is a TODO

[maxulysse]

Description of the bug

Some of the content of the RO-crate appears in the nf-core lint warning without any explanation.
It took me a while to realize it was coming from this file, as I was cleaning up the README and the text was still the same 😆

Command used and terminal output

╭─ [!] 9 Pipeline Test Warnings ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
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│ 🌆 GitHub Actions CI Status 🌆 GitHub Actions Linting Status 🌆 AWS CI 🌆 Cite with Zenodo 🌆 nf-test 🌆 Nextflow 🌆 run with conda 🌆 run with docker 🌆 run with singularity 🌆 Launch o │
│ <img alt="nf-core/references" src="docs/images/nf-core-references_logo_light.png">\n  \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n## Introduction\n\nnf-core/references is a bioinformatics    │
│ pipeline that build references, for multiple use cases.\n\nIt is primarily designed to build references for common organisms and store it on AWS iGenomes.\n\nFrom a fasta file, it will   │
│ be able to build the following references:\n\n- Bowtie1 index\n- Bowtie2 index\n- BWA-MEM index\n- BWA-MEM2 index\n- DRAGMAP hashtable\n- Fasta dictionary (with GATK4)\n- Fasta fai (with │
│ SAMtools)\n- Fasta sizes (with SAMtools)\n- Fasta intervals bed (with GATK4)\n- MSIsensor-pro list\n\nWith an additional annotation file describing the genes (either GFF3 or GTF), it     │
│ will be able to build the following references:\n\n- GTF (from GFF3 with GFFREAD)\n- HISAT2 index\n- Kallisto index\n- RSEM index\n- Salmon index\n- Splice sites (with HISAT2)\n- STAR    │
│ index\n- Transcript fasta (with RSEM)\n\nWith a vcf file, it will compress it, if it was not already compressed, and tabix index it.\n\n## Assets\n\nAssets are stored in                  │
│ references-assets.\n\n## Running\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\nasset.yml:\n\nyml\n- genome: GRCh38_chr21\n  fasta:                                                                                    │
│ \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.fa\"\n  gtf:                                                                     │
│ \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/GRCh38_chr21.gtf\"\n  source_version: \"CUSTOM\"\n  readme:                                   │
│ \"https://raw.githubusercontent.com/nf-core/test-datasets/references/references/GRCh38_chr21/README.md\"\n  source: \"nf-core/references\"\n  source_vcf: \"GATK_BUNDLE\"\n  species:      │
│ \"Homo_sapiens\"\n  vcf: \"https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz\"\n\n\nEach line represents a       │
│ source for building a reference, a reference already built or a metadata.\n\nNow, you can run the pipeline using:\n\nbash\nnextflow run nf-core/references \\\n   -profile                 │
│ <docker/singularity/.../institute> \\\n   --input asset.yml \\\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/references was originally written by Maxime U Garcia | Edmund Miller | Phil Ewels.\n\nWe thank the following people for their extensive assistance in the development   │
│ of this pipeline:\n\n- Adam Talbot\n- Friederike Hanssen\n- Harshil Patel\n- Jonathan Manning\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 #references channel (you can join with this invite).\n\n### How to hack   │
│ on it\n\n0. Have docker, and Nextflow installed\n1. nextflow run main.nf\n\n### Some thoughts on reference building\n\n- We could use the glob and if you just drop a fasta in s3 bucket   │
│ it'll get picked up and new resources built\n  - Could take this a step further and make it a little config file that has the fasta, gtf, genome_size etc.\n- How do we avoid rebuilding?  │
│ Ideally we should build once on a new minor release of an aligner/reference. IMO kinda low priority because the main cost is going to be egress, not compute.\n- How much effort is too    │
│ much effort?\n  - Should it be as easy as adding a file on s3?\n    - No that shouldn't be a requirement, should be able to link to a reference externally (A "source of truth" ie an FTP  │
│ link), and the workflow will build the references\n    - So like mulled biocontainers, just make a PR to the samplesheet and boom new reference in the s3 bucket if it's approved?\n\n###  │
│ Roadmap\n\nPoC for v1.0:\n\n- Replace aws-igenomes\n  - bwa, bowtie2, star, bismark need to be built\n  - fasta, gtf, bed12, mito_name, macs_gsize, blacklist, copied over\n\nOther nice   │
│ things to have:\n\n- Building our test-datasets\n- Down-sampling for a unified genomics test dataset creation, (Thinking about viralitegration/rnaseq/wgs) and spiking in test cases of    │
│ interest (Specific variants for example)\n\n## Citations\n\nIf you use nf-core/references for your analysis, please cite it using the following doi: 10.5281/zenodo.14576225\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",                                      │

System information

No response

[ewels]

• Ignore the RO crate for linting
• Sync the RO crate with the README.md better to make sure that the two are in step
  • Add a lint test that checks that the two are in sync. Allow --fix to clobber and rewrite.