nf-jabba encountered an error while starting with the BAM files.

[rajithadp]

Description of the bug

I want to use nf-jabba to generate Jabba calls for my BAM files. I followed the usage instructions, and as I understood them, I used the appropriate commands. The pipeline was completed without errors; however, each tool has no results in my output directory.

Command used and terminal output

nextflow run mskilab-org/nf-jabba \
   -profile singularity \
   --input samplesheetV2.csv \
   --outdir OUTDIR \
   --tools svaba,fragcounter,dryclean,cbs,hetpileups,ascat,jabba \
   --genome GRCh38 \
   --step sv_calling

Relevant files

System information

N E X T F L O W ~ version 24.04.4

Input/output options
input : samplesheetV2.csv
step : sv_calling
outdir : OUTDIR

Main options
tools : svaba,fragcounter,dryclean,cbs,hetpileups,ascat,jabba

Preprocessing
save_mapped : true
save_output_as_bam : true

HetPileUps
hapmap_sites : null

FragCounter
midpoint_frag : TRUE
paired_frag : TRUE
exome_frag : FALSE
minmapq_frag : 60

Dryclean
build_dryclean : null

JaBbA
blacklist_junctions_jabba : NULL
slack_jabba : 20
linear_jabba : FALSE
epgap_jabba : 0.000001
blacklist_coverage_jabba : null

Reference genome options
genome : GRCh38
bwa : s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/
fasta : s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
igenomes_base : s3://ngi-igenomes/igenomes
mski_base : s3://mskilab-pipeline