Stephen Watts
Stephen Watts
Agreed, this will be implemented in oncoanalyser in due course! I'll leave the issue open until that piece of work is complete
Hi @bounlu, this is an issue that I've run into myself and have thought about ways to solve, including an approach similar to your suggestion. For the oncoanalyser 1.0.0 release...
This will be reviewed after the upcoming release, de-scoping from that release accordingly
Hi @fevac, thanks for reporting this. I've been able to run an oncoanalyser 2.2.0 'wgts' analysis with a tumour-only input, so I suspect this is error is related to your...
Thanks for the information, I'll get in contact with you on Slack to send the log file
Additionally where a samplesheet has FASTQ input files provided as separate entries rather than the expected single entry, an informative error should be provided. See: https://nfcore.slack.com/archives/C04CQ1LK7U1/p1734010565913889
Hi @RP-Silk, can you please post your configuration files, samplesheet, and the `params.csv` file?
If I recall correctly the GEL reference genome used to generate the read alignments with DRAGEN includes ALTs, which is not compatible with the `GRCh38_hmf` reference genome This is likely...
Hi @silkrp, sorry for the slow response! The `--ref_data_genome_alt` parameter is used only when creating indexes (e.g. BWA-MEM2, GRIDSS, etc) for a given reference FASTA file, and the parameter expects...
Thanks for the update and all the additional information. I still suspect this is most likely caused by a mismatch between contigs in the reference genomes used for alignment and...