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Sample naming fixes #121

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@pontushojer pontushojer commented Jul 9, 2025 •
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fix #105 and some naming improvements, esp for MultiQC reports.

This PR modifies sample indexes to include leading zeros. To allow for multiple sample sharing the same sample name (meta.sample) the sample id (meta.id) has a suffix (_#) corresponding to its row number in the samplesheet. This is used in the file naming and the MultiQC report. The issue with this is that a single end sample sample_1 would get the id sample_1_1 which would be the same id read1 of the paired end sample sample would get. To make it clear which part refers to the sample index and the read I have added leading zeros to the indices.

sample_1 -> sample_1_01 for a single end sample
sample -> sample_01_1 for read1 in a paired end sample

It is now clear what part of the suffix refers to the index (01) and a possible read number (1).

In the MultiQC report I have also modified the names using the sample_names_replace config option to clearly separate between the sample name given in the samplesheet and any suffix appended by the seqinspector workflow.

Here is an example of what this looks like with a samplesheet containing three single end samples with one appearing twice (e.g. a rerun).

before (dev)

sample name (from samplesheet) sample id in MultiQC report
sample_1 sample_1_1 sample_1_1
sample_2 sample_1_2 sample_1_2
sample_3 sample_1_3 sample_1_3

after (this PR)

sample name (from samplesheet) sample id in MultiQC report
sample_1 sample_1_01 sample_1 #01
sample_2 sample_1_02 sample_1 #02
sample_3 sample_1_03 sample_1 #03

Examples of what the MultiQC report looks like now are show below

The only tool which still has ugly names is seqfu stats, but this could be fixed once #126 is done.

Paired end example

Here are the samples included

% cut -f 1 -d, nfcore-test-datasets-seqinspector/testdata/Miseq_PairedEnd/samplesheet.csv 
sample
SAMPLE_PAIRED_END_1
SAMPLE_PAIRED_END_2

General Stats

before
image

after
image

FastQC

before
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after
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FastqScreen

before
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after
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Single end example

% cut -f 1 -d, nfcore-test-datasets-seqinspector/testdata/Miseq/samplesheet.csv
sample
SAMPLE_SINGLE_END

General stats

before
image

after
image

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/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

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nf-core-bot commented Jul 9, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@pontushojer pontushojer changed the title Sample naming fixes WIP: Sample naming fixes Jul 22, 2025
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github-actions bot commented Aug 8, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 69e4948

+| ✅ 189 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ Test warnings:

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❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-10-07 12:32:03

@pontushojer pontushojer changed the title WIP: Sample naming fixes Sample naming fixes Oct 7, 2025
@FranBonath FranBonath added this to the 1.0.0 milestone Nov 6, 2025
@FranBonath FranBonath moved this to optional (non-ciritical) in seqinspector project board Nov 7, 2025
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Use MultiQC feature to merge paired-end sample rows in report tables

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@pontushojer @nf-core-bot @FranBonath