Add clustering test tsv - #2073
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Add other input types to test pbmarkdup modules
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
sarscov2mouse
…roteomics section alphabetically
added interproscan mini test data
feat: add check2 tsv for galah
bigslice test dataset
Extend paraphase configuration
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
Code review for nf-core#1863
ips result test file for post-processing software
added test data files for pharmcat module
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
This is required for nf-core/modules#11365.
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
…testdata Add savana classify testdata
…stdata Add test data for octopusv/plot
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Add test dataset for pcaclustering
This PR adds a new minimal dataset (
test.tsv) for thepcaclusteringfunctionality 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
pcaclusteringlogic in nf-core modulestest_features.tsv,test_clusters.csv, etc.)Dataset generation
The
test.tsvfile was generated fromtest.eigenvecusing the followingawkcommand: