Error: with the current options, either 'chrFiles' or 'GCcontentProfile' must be set

[drkoryjohns]

Description of the bug

Hello,

Trying to run controlfreec option in sarek pipeline on rat:

vi samplesheet.csv

patient,sex,status,sample,lane,bam,bai rat1,XX,1,tumor_sample,lane_1,/data/johnsonko/Analysis_Projects/Sadhana_Jackson/WGS_20240226/preprocessing/recalibrated/tumor_sample/tumor_sample.recal.bam,/data/johnsonko/Analysis_Projects/Sadhana_Jackson/WGS_20240226/preprocessing/recalibrated/tumor_sample/tumor_sample.recal.bam.bai

:wq!

vi nf_core_sarek_go.swarm

nextflow run nf-core/sarek -r 3.4.0 --input samplesheet.csv --outdir . --step variant_calling --fasta Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa --fasta_fai Rattus_norvegicus.mRatBN7.2.dna.toplevel.fa.fai --dbsnp rattus_norvegicus.vcf.gz --known_snps rattus_norvegicus.vcf.gz --tools controlfreec -profile biowulf --igenomes_ignore --genome null

:wq!

swarm -f nf_core_sarek_go.swarm -g 200 --gres=lscratch:200 --time 36:00:00 -t 24 --module nextflow,singularity

... getting error:

Error: with the current options, either 'chrFiles' or 'GCcontentProfile' must be set

... I do not see 'chrFiles' as a parameter option.

Need help/guidance please.

Thank you!

Command used and terminal output

No response

Relevant files

No response

System information

No response

[nschcolnicov]

Hi @drkoryjohns this happened to me too, there is a parameter for chr_dir that you need to add, which should contain a list of fasta files, one for each chromosome of your reference fasta. You can see it in the igenomes config file: https://github.com/nf-core/sarek/blob/master/conf/igenomes.config

For example this is what that chr_dir looks like (aws s3 ls s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh37/Sequence/Chromosomes/):

TLDR: You can add the chr_dir using --chr_dir, if you want to see how the parameters are fetched from igenomes you can see it being done here: https://github.com/nf-core/sarek/blob/master/main.nf using the getGenomeAttribute from https://github.com/nf-core/sarek/blob/master/lib/WorkflowMain.groovy