Error in parsing ${cancer}

[RyulKim-Inocras]

Thank to your help, I succeded to complete the intogen pipeline on my samples.
But I encounterd a small issue that might affect the final output.

The "cohort.tsv" file shows

COHORT CANCER_TYPE PLATFORM MUTATIONS SAMPLES
XXXXX AAAAAA.parsed.tsv.gz
BRCA WGS 847284 1505

But, I think it should be like this

COHORT CANCER_TYPE PLATFORM MUTATIONS SAMPLES
XXXXX BRCA WGS 847284 1505

In other words,
The ${cancer} in intogen.nf shoud be "BRCA", but wronlgy parsed into "AAAAAA.parsed.tsv.gz\nBRCA"
(note line separator between AAAAAA.parsed.tsv.gz and BRCA!!!!)

This lead an error in DriverDiscovery step, because the option --ctype became

--ctype AAAAAA.parsed.tsv.gz <- line seperator here!!
BRCA

and 'BRCA' is not a excutable command.

I tweaked this problem by editing the DriverDiscovery step as follows:

--ctype ${cancer} --> --ctype BRCA

But still, because cohort.tsv is used in DriverSummary step,
This seems affect the final output including "drivers.tsv" as all the 'CANCER_TYPE' and '_SAMPLES_COHORT' columns in the file shows 'AAAAAA.parsed.tsv.gz' and 'NA' respectively.
I thinks they should be

CANCER_TYPE : 'BRCA' instead of 'AAAAAA.parsed.tsv.gz'
%_SAMPLES_COHORT : the number in SAMPLES column divived by total number of samples (1505 in my case)

How can I solve this minor (potentially major..?) issue?
Do you think this behavior affect any other critical steps other than 'drivers.tsv' and 'cohort.tsv.' files in pipeline?

FYI, my yaml file looks like this

• type: static
  field: DONOR
  value: '{SAMPLE}'
• type: static
  field: CANCER
  value: BRCA
• type: static
  field: PLATFORM
  value: WGS

Regards,

[FedericaBrando]

Hi @RyulKim-Inocras,

you need to specify the "DATASET" field in the yml:

for example:

- type: static
  field: DATASET
  value: dataset1_{PLATFORM}_{CANCER}_YYYY

[RyulKim-Inocras]

Dear Federica,

Yes I have DATASET field in my yaml

Here is my full metadata.yaml (basically sames as the one in the test folder of intogen)
Please find the attached file. (The file extension was change from yaml to txt to upload)

metadata.txt