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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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samplesheet verification failed when running variant_calling step #997

Open paumarc opened 1 year ago

paumarc commented 1 year ago

Description of the bug

i runned sarek to performe a variant calling with a wrong samle file and the samplesheet was not correctly verified

Command used and terminal output

nextflow run nf-core/sarek -profile singularity --input results_CRESPOMAR_06/csv/markduplicates.csv --genome hg19 -r 3.1.2 -c sarek.conf --outdir results_CRESPOMAR_06 --pon /mnt/bioinfnas/bioinformatics/projects/20220808_MCrespo_22LLC/Mutect2-hg19-exome-panel.vcf.gz --known_indels /mnt/bioinfnas/bioinformatics/projects/20220808_MCrespo_22LLC/Mills_and_1000G_gold_standard.indels.b37.vcf.gz --tools mutect2,strelka,snpeff,vep --igenomes_base /mnt/bioinfnas/general/refs/igenomes/ --step variant_calling

Relevant files

No response

System information

using singularity 3ea83f6-dirty

FriederikeHanssen commented 1 year ago

Hi! I need more info: the samplesheet and what exactly the issue was :)