Provide test data

[richelbilderbeek]

Dear nextNEOpi maintainers,

Thanks for nextNEOpi, it seems like a useful tool!

However, I would have enjoy to have seen some more simulated/public example data, so anyone can verify that everything works as it should be. I see that there are some example files, but running it fails.

For example, when running ...

nextflow run nextNEOpi.nf --batchFile example_batchFile_FASTQ.csv \
  -profile singularity \
  -config conf/params.config \
  --exomeCaptureKit "Twist" \
  --trim_adapters true \
  --trim_adapters_RNAseq true \
  --mutect2ponFile 1000g_pon.hg38.vcf.gz \
  --use_sequenza_cnvs true \
  --TCR false \
  --accept_license

... then these files are needed as well:

• reads_s1_t_1.fastq.gz
• reads_s1_t_2.fastq.gz
• reads_s1_n_1.fastq.gz
• reads_s1_n_2.fastq.gz
• reads_s1_r_1.fastq.gz
• reads_s1_r_2.fastq.gz
• data/sample2_hla.txt

It would be great to have simulated/public data added, among others to add Continuous Integration and/or help users report bugs.

For me, this script really looks a bit too clumsy :-/

Thanks and cheers, Richel Bilderbeek

[richelbilderbeek]

See also https://github.com/hammerlab/wobidisco/issues/8

[richelbilderbeek]

See also https://github.com/jiujiezz/tsnad/issues/32

[riederd]

Hi,

thanks for your interest in nextNEOpi and for your suggestion to include test data. We will consider it for future releases. For now we only test with our in house patient data which - due to privacy reasons - we can not share.

[richelbilderbeek]

Note to self: testing datasets can be found at https://github.com/nf-core/test-datasets

[riederd]

closed by 92712e0748a9cc1b0ec5755e2d0c9f5d46a224fa