Error with Index Out of Bounds When Running Sarek WES Pipeline with Tools Enabled (e.g., Mutect2)

[kristianunger]

Description of the bug

When running the Sarek pipeline on WES data without specifying any tools, the pipeline executes without issues. However, when adding one or more tools, such as --tools mutect2, the pipeline fails with an error:

ERROR ~ Index 1 out of bounds for length 1

 -- Check script '/home/kunger/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_intervals/main.nf' at line: 80 or see '.nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details

Environment Details:

•   Sarek version: 3.4.4
•   Nextflow version: 24.04.4
•   Singularity profile
•   Reference genome: GATK.GRCh38
•   Intervals file: S07604514_Covered.bed
    •   java 17.0.12 2024-07-16 LTS

Command used and terminal output

runs smoothly:

NXF_VER=24.04.4 nextflow run nf-core/sarek -r 3.4.4 -profile singularity --input ./sample_sheet.csv --outdir ./results --genome GATK.GRCh38 --wes TRUE --intervals /train_data/kunger/Agilent_intervals/S07604514_Covered.bed

results in error:

NXF_VER=24.04.4 nextflow run nf-core/sarek -r 3.4.4 -profile singularity --input ./sample_sheet.csv --outdir ./results --genome GATK.GRCh38 --wes TRUE --intervals /train_data/kunger/Agilent_intervals/S07604514_Covered.bed --tools mutect2

Relevant files

nextflow.log

System information

No response

[kristianunger]

Was able to solve myself. The target file contained a header and removing this header fixed the problem.