I am getting an error when trying to run

oncoanalyser

which is:

ERROR ~ got unexpected subject name for EPN-CNN BT366: BT400

 -- Check '.nextflow.log' file for details

samplesheet.csv

group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
EPN-CNN,BT366,BT366-EPN-CNN,tumor,dna,fastq,library_id:S1;lane:001,~/00137-3_S3_L01_R1_001.fastq.gz;~/00137-3_S3_L01_R2_001.fastq.gz
EPN-CNN,BT400,BT400-EPN-CNN,tumor,dna,fastq,library_id:S1;lane:002,~/00137-4_S4_L01_R1_001.fastq.gz;~/00137-4_S4_L01_R2_001.fastq.gz
EPN-1q6q,BT609,BT609-EPN-1q6q,tumor,dna,fastq,library_id:S1;lane:001,~/00137-1_S1_L01_R1_001.fastq.gz;~/00137-1_S1_L01_R2_001.fastq.gz

Does anyone know if I am setting up my samplesheet incorrectly?

Hi Cathal, rows 1 and 2 share group_id EPN-CNN but have different subject_id values (BT366 vs BT400). Since these appear to be independent tumor-only samples (no normal/pair relationship), each should be its own group so you can either give them different group_ids or identical subject_ids, depending on whether these samples belong together or not

That worked, thanks @Rayan Hassaïne Does

oncoanalyser

run all the listed tools (SAGE, AMBER etc) by default? I know that they can be turned off with

--processes_exclude

The samples I am running are old tumour samples from FFPE tissues and some of them will be chosen for further spatial profiling later. We want the samples with the most amount of tumour. Would the

purity_estimate

give something like that? Or any other output from the pipeline?

yes, it runs them with slight differences depending on the different types of analyses you're performing (tumor + normal pair, tumor-only, dna, rna, etc). You can most definitely select which steps run with this flag (among others) and PURPLE is our tool for purity and ploidy estimation. That output will be both in that tool's directory output and the ORANGE report.

Purity_estimate

is another mode used for tumor fraction estimation with a longitudinal sample like ctDNA