Pipeline crashes when supplying bwa_index with circular mapper

[scarlhoff]

Hi!
As the name suggests, my eager2 session was aborted when I supplied bwa_index despite using circular mapper for mitochondrial capture data.

Nov-13 14:09:00.144 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'bwa_index'

Here is the command
nextflow run nf-core/eager -r 2.2.1 -c ~/eager2.config -profile humanMT,sdag,shh --input MTcap.tsv

and profile I was using:
profiles { humanMT { params { config_profile_description = "human MT data HG19 SE" config_profile_contact = "Selina Carlhoff (@scarlhoff)" fasta = "/projects1/Reference_Genomes/Human/HG19/hg19_MT.fasta" fasta_index = "/projects1/Reference_Genomes/Human/HG19/hg19_MT.fasta.fai" bwa_index = "/projects1/Reference_Genomes/Human/HG19/" seq_dict = "/projects1/Reference_Genomes/Human/HG19/hg19_MT.dict" skip_preseq = true clip_readlength = 0 preserve5p = true mapper = "circularmapper" circulartarget = "NC_012920.1" run_bam_filtering = true bam_mapping_quality_threshold = 30 bam_filter_minreadlength = 25 bam_unmapped_type = "discard" } } }
Thanks!

[jfy133]

I think due to:

eager/main.nf

Line 331 in 7971d89

if( params.bwa_index != '' && (params.mapper == 'bwaaln' | params.mapper == 'bwamem')){