Can not find BAM in Sentieon branch #192
Description
My guess it is a typo
szilva@munin /data2/sentieon/P2233/P2233_101T_P2233_120N $ nextflow run MaxUlysse/nf-core_sarek -r Sentieon -profile munin --input ../tsv/P2233_101T_P2233_120N.tsv --steps mapping,variantcalling --tools TNScope --skip_qc all --sentieon
N E X T F L O W ~ version 19.10.0
Launching `MaxUlysse/nf-core_sarek` [backstabbing_colden] - revision: 428036b186 [Sentieon]
...
[fc/b4266c] Submitted process > MergeBamMapped (Sent_P2233_101T_120N-P2233_120N)
Error executing process > 'IndexBamMergedForSentieon (Sent_P2233_101T_120N-P2233_120N)'
Caused by:
Unknown variable 'bam' -- Make sure it is not misspelt and defined somewhere in the script before using it
Source block:
"""
samtools index ${bam}
"""