Description of the bug

Hello,

I hope you're doing well. I’m a bit confused with a question. I ran the pipeline using the GRCh38 reference genome and Mutect2 in paired tumor-normal files. The entire pipeline completed successfully using nf-sarek version 3.4.3.

However, I’m unsure where I can find the folder or file that contains information about the coverage and depth of the sequences.

I apologize if this is a basic question, and I really appreciate your help.

Thank you!

Command used and terminal output

nextflow run /slgpfs/projects/cli20/cli20901/soft/nf-core-sarek_3.4.3/3_4_3/main.nf -profile singularity --input ./ID091.csv --outdir ./results_ID091 --max_cpus 40 --genome GRCh38 --ngscheckmate_bed false --igenomes_base ./references --wes --tools mutect2

Relevant files

No response

System information

Nextflow v.23.04
Hardware HPC
Executor Slurm
Container engine Singularity
Version of nf-core/sarek 3.4.3