Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

Hello @drpatelh and @KevinMenden,

Thank you for maintaining the RSeQC modules — your work is much appreciated.

I’m currently using them and the modules are producing the expected outputs. However, the underlying logs indicate that a BAM index (.bai) is expected. When I provide only the BAM file as input, the Python tools run successfully but emit warnings about a missing .bai index.

    RSEQC_INNERDISTANCE(BAM_SORT_STATS_SAMTOOLS.out.bam, bed)
    RSEQC_INFEREXPERIMENT(BAM_SORT_STATS_SAMTOOLS.out.bam, bed)
    RSEQC_READDISTRIBUTION(BAM_SORT_STATS_SAMTOOLS.out.bam, bed)
    RSEQC_JUNCTIONSATURATION(BAM_SORT_STATS_SAMTOOLS.out.bam, bed)

The error is:

 // [E::idx_find_and_load] Could not retrieve index file for 'example.Aligned.out.bam'

Should the inputs for these modules be expanded to include the .bai file?
ie:
from:

    input:
    tuple val(meta), path(bam)
    path  bed

to:

    input:
    tuple val(meta), path(bam), path(bai)
    path  bed

Command used and terminal output

#!/usr/bin/env bash -C -e -u -o pipefail
infer_experiment.py \
    -i example.bam \
    -r gencode.v38.annotation.bed \
    -s 3000000 -q 1 \
    > example.infer_experiment.txt

Relevant files

No response

System information

N E X T F L O W ~ version 25.04.6