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Change schema meta - #88

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KateSakharova merged 8 commits into
fix/docs-reviewfrom
fix/meta_objects
Jul 27, 2026
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Change schema meta#88
KateSakharova merged 8 commits into
fix/docs-reviewfrom
fix/meta_objects

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@KateSakharova

@KateSakharova KateSakharova commented Jul 21, 2026 •
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@KateSakharova KateSakharova changed the title rename sample to id in samplesheet and add fields to meta directly fr… Change schema meta Jul 21, 2026
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KateSakharova marked this pull request as ready for review July 21, 2026 19:59
@KateSakharova KateSakharova mentioned this pull request Jul 22, 2026
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mberacochea
mberacochea reviewed Jul 22, 2026
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Comment thread assets/schema_input_genome.json Outdated
mberacochea
mberacochea reviewed Jul 22, 2026
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Comment thread assets/schema_input_reads.json Outdated
mberacochea
mberacochea reviewed Jul 22, 2026
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Comment thread workflows/assemblysubmit.nf Outdated
mberacochea
mberacochea reviewed Jul 22, 2026
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Comment thread workflows/genomesubmit.nf Outdated
mberacochea
mberacochea reviewed Jul 22, 2026
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Comment thread workflows/assemblysubmit.nf Outdated
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mberacochea reviewed Jul 22, 2026
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Comment thread workflows/readsubmit.nf Outdated
mberacochea
mberacochea approved these changes Jul 22, 2026
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@mberacochea mberacochea left a comment

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Thanks @KateSakharova

I've left some very minor comments

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github-actions Bot commented Jul 22, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit edd594a

+| ✅ 251 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
Details

❗ 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
  • container_configs - container_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.2
  • Run at 2026-07-23 13:48:34

@KateSakharova
KateSakharova requested a review from ochkalova July 23, 2026 13:30
ochkalova
ochkalova approved these changes Jul 27, 2026
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@ochkalova ochkalova left a comment

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Amazing work! So much cleaner now 👏🏻

Comment thread assets/schema_input_genome.json Outdated
Comment on lines +119 to +120
"type": "number",
"minimum": 0

@ochkalova ochkalova Jul 27, 2026

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coverage = 0 will fail ENA validation
would be good to add some check that it's > 0 if it's possible

@KateSakharova KateSakharova Jul 27, 2026

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yeah, good catch, changed to exclusiveMinimum

Comment thread assets/schema_input_genome.json
Comment on lines 30 to 45
"fastq_1": {
"anyOf": [
{
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.(fq|fastq)(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
],
"errorMessage": "FASTQ file must have extension '.fq' or '.fastq' (optionally gzipped)",
"description": "Forward reads if paired-end or single-end reads FASTQ file"
},

@ochkalova ochkalova Jul 27, 2026

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I think this one also requires default = null, or not? 🤔

@KateSakharova KateSakharova Jul 27, 2026

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true, I forgot is it also not required value

@KateSakharova
KateSakharova merged commit fb2db68 into fix/docs-review Jul 27, 2026
18 of 21 checks passed
@KateSakharova
KateSakharova deleted the fix/meta_objects branch July 27, 2026 14:20
@KateSakharova KateSakharova mentioned this pull request Jul 27, 2026
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@mberacochea mberacochea mberacochea approved these changes
@ochkalova ochkalova ochkalova approved these changes
@timrozday-mgnify timrozday-mgnify Awaiting requested review from timrozday-mgnify

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@KateSakharova @mberacochea @ochkalova