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TheJacksonLaboratory / cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines
MIT License
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WGS pipeline error #7

Closed lawtyunc closed 1 month ago

lawtyunc commented 1 month ago

Hi Jackson Lab, I was running your cs-nf-WGS pipeline and getting the following error

ERROR ~ Error executing process > 'WGS:BWA_MEM (S*)'

Caused by: Process `WGS:BWA_MEM

Command executed:

rg=$(cat S*read_group.txt) bwa mem -R ${rg} -t 12 -B 8 path/to/Mus_musculus.GRCm39.dna.toplevel.fa.fai

the confusing part is the input wants a fasta index file but in the documentation is asking for a fasta file wasn't sure if this was a typo or how we could get around this error?

--ref_fa_indices

Default: '/projects/omics_share/mouse/GRCm38/genome/indices/ensembl/v102/bwa/Mus_musculus.GRCm38.dna.toplevel.fa' Comment: Pre-compiled BWA index files, points to human reference when * --gen_org human. JAX users should not change this parameter.

MikeWLloyd commented 1 month ago

ref_fa_indices should point to BWA index files and not the .fai file.

Generate BWA indecies with the tool (i.e., bwa index ref.fa) and then set ref_fa_indices to the path and base file name of the index files.