Hi everyone, as a new user I would just first like to say thank you for the amazing tool. I wanted to run oncoanalyser from two different starting points. I have the normal samples already aligned, but not the tumor samples. However, I'm getting an error during validation where it says that it can't find the redux bams and tsvs in the same directory

ERROR ~ When only specifying filetype BAM_REDUX in the sample sheet, make sure the REDUX BAM and TSVs are in the same dir:
<s3://bucket/oncoanalyser/PDO/alignments/dna/normal-sample.redux.bam> (BAM_REDUX)
/bucket/oncoanalyser/PDO/alignments/dna/normal-sample.jitter_params.tsv (missing expected REDUX_JITTER_TSV)
/bucket/oncoanalyser/PDO/alignments/dna/normal-sample.ms_table.tsv.gz (missing expected REDUX_MS_TSV)
Alternatively, provide the TSV paths in the sample sheet using filetype values: REDUX_JITTER_TSV, REDUX_MS_TSV

Is anything wrong with my samplesheet? Is it possible to have two different starting points for different sample types in the same samplesheet?

Hi @Mafalda Soares, this should be possible and your samplesheet looks correct at a glance

Sorry, it was a mistake on my part, the real filepaths were not correct. Thank you for your help!

No worries, glad to hear it was an easy fix!