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Add full Bowtie2 index and reference FASTA for host contamination testing - #4

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fastp-test-data
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Add full Bowtie2 index and reference FASTA for host contamination testing#4
Alexaz13 wants to merge 4 commits into
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fastp-test-data

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@Alexaz13

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This PR adds the necessary files to support nf-test testing of the bowtie2_align module with the PolyBio dataset. Specifically, it includes:

  • A full Bowtie2 index (hg38.*.bt2 files) for the human genome.
  • The matching reference FASTA file (GCA_009914755.4_T2T-CHM13v2.0_genomic.fna).

These files were added in accordance with nf-core guidelines for test datasets.

Purpose

These additions will allow us to:

  • Perform host contamination filtering tests using real paired-end FASTQ data.
  • Validate the functionality of the bowtie2_align module using human reference genome alignment.

Notes

  • Files are hosted under polybio/host/ and polybio/ncbi_genome/ to maintain organization.
  • The FASTA and index files match and were sourced from NCBI (T2T-CHM13v2.0).
  • Large files were pushed in batches to avoid timeouts.

@411an13

411an13 commented Aug 14, 2025

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We shouldn't merge the test data to master. Each pipeline has a dedicated branch (and a special one for modules).

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