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Add clustering test tsv - #2073

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Add clustering test tsv#2073
dbaku42 wants to merge 2064 commits into
nf-core:masterfrom
dbaku42:add-clustering-test-tsv

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@dbaku42 dbaku42 commented May 22, 2026

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Add test dataset for pcaclustering

This PR adds a new minimal dataset (test.tsv) for the pcaclustering functionality within the clustering test suite.

The dataset is added under:

data/genomics/homo_sapiens/popgen/clustering/

and is intended to support reproducible unit testing of PCA-based clustering workflows.

This addition is related to:
nf-core/modules#11372

Purpose

  • Enable robust testing of pcaclustering logic in nf-core modules
  • Provide a minimal, reproducible input dataset for CI and nf-test execution
  • Ensure compatibility with existing clustering test assets (test_features.tsv, test_clusters.csv, etc.)

Dataset generation

The test.tsv file was generated from test.eigenvec using the following awk command:

awk 'NR==1 {
  sub(/^#/, "");
  $1 = "";
  sub(/^\t/, "");
  sub(/^IID\t/, "sample_id\t");
  print;
  next
}
{
  $1 = "";
  sub(/^\t/, "");
  print
}' OFS='\t' test.eigenvec > test.tsv

tckumarasekara and others added 30 commits January 24, 2026 22:13
Add other input types to test pbmarkdup modules
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
added interproscan mini test data
add test files for hifitrimmer filterbam
RSEM results (genes.results + isoforms.results) for 3 samples
(WT_REP2, RAP1_UNINDUCED_REP1, RAP1_IAA_30M_REP1) from the
GSE110004 yeast dataset, quantified against the same reference
used by the existing salmon and kallisto result archives.

Used by nf-core/rnaseq quant_tximport_summarizedexperiment
subworkflow tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  Data for testing the rgi modules. See nf-core/modules#9873 for discussion.
  Add information about new rgi directory. Code review for nf-core#1863.
Add RSEM quantification results for S. cerevisiae
ips result test file for post-processing software
 added test data files for pharmcat module
dbaku42 and others added 29 commits May 15, 2026 21:57
Updated README to clarify test file generation and usage.
Add genomics/virus/influenza/fasta/H5N1_Italy.fa
…test-data

Add test data for virusrecom module
Mock gene family abundance data to test the HUMAnN3 module
Add a list of transcription start sites on chr22
…est-data

Add mock gene family abundance data
Co-authored-by: Jonathan Manning <pininforthefjords@gmail.com>
Add test data for custom/clustering, clustermetrics and clustervisualization
Four Ribo-seq samples downsampled to chr19+chr22 protein-coding-gene
loci, with a protein-coding-only reference. Sized so every file is
under 4 MiB and PRICE still produces a non-empty orfs.tsv (381 lines).

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds an entry under genomics/homo_sapiens/riboseq_expression for the new
price/ fixtures, matching the existing plastid/ and ribocode/ block style.
Notes why a second chromosome (chr19+chr22) and 4-sample cohort are
needed - PRICE's candidate-ORF count and noise-model floor.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Replaced the reference to "Seqera Platform stage commit c4cb19dc" with
the persistent SRA accession trail (SRR15480788/9/90/91 from GSE182201)
plus the alignment tooling. The Platform workdir wouldn't be reachable
to anyone reading this README later.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Add gedi/price test data: chr19+chr22 Ribo-seq cohort
Add BED test data for cnvkit/coverage version 0.9.13
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