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Add tutorial demonstrating how to convert a NCBI assembly_summary file to a nf-core/createtaxdb samplesheet #144

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Add tutorial demonstrating how to convert a NCBI assembly_summary file to a nf-core/createtaxdb samplesheet #144

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@jfy133 jfy133 commented Jan 6, 2026

  • Partial code assistance by Claude Haiku for one AWK command
  • Documentation style reviewed by GPT 5.1 Codex Max against alpha nf-core style guide from @christopher-hakkaart

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/createtaxdb branch on the nf-core/test-datasets repository.
  • 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).

@jfy133
Add tutorial page for creating samplesheets from NCBI assembly_summar…
9c39be8 
…y.txt (code assistance by Claude Haiku, and documentation style reviewed by GPT 5.1 Codex Max against alpha nf-core style guide from @christopher-hakkaart)
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github-actions bot commented Jan 6, 2026 •
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nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit cc3d7c7

+| ✅ 227 tests passed       |+
#| ❔   2 tests were ignored |#
#| ❔   1 tests had warnings |#
Details

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-06 10:39:30

dialvarezs
dialvarezs approved these changes Jan 8, 2026
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Works for me!

Personally, I would make the awk expression more legible, but not a blocker

docs/usage/tutorials.md
4. Reconstruct the complete URLs of the relevant FASTA files to make them downloadable.

```bash
awk 'BEGIN { FS=OFS="\t" } NR > 1 { n=split($3,p,"/"); $4=$3"/"p[n]"_protein.faa.gz"; $3=$3"/"p[n]"_genomic.fna.gz"} {print $1","$2","$3","$4}' assembly_summary_simplified.txt > samplesheet.csv
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@dialvarezs dialvarezs Jan 8, 2026 •
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Suggested change
awk 'BEGIN { FS=OFS="\t" } NR > 1 { n=split($3,p,"/"); $4=$3"/"p[n]"_protein.faa.gz"; $3=$3"/"p[n]"_genomic.fna.gz"} {print $1","$2","$3","$4}' assembly_summary_simplified.txt > samplesheet.csv
awk 'BEGIN { FS="\t"; OFS="," }
NR>1 {
base=$3; sub(".*/","",base)
$4=$3 "/" base "_protein.faa.gz"
$3=$3 "/" base "_genomic.fna.gz"
}
{ print $1,$2,$3,$4 }' assembly_summary_simplified.txt > samplesheet.csv

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