bam_tumor_only_somatic_variant_calling_gatk: Input channel structure mismatch for ch_fai between MUTECT2 and GETPILEUPSUMMARIES

Have you checked the docs?

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

Description of the bug

I encountered an input tuple mismatch error when running the bam_tumor_only_somatic_variant_calling_gatk subworkflow.

The issue stems from a conflict in how the reference index (ch_fai) is defined in the input blocks of the two underlying modules:

GATK4_MUTECT2 requires a 3-element tuple: tuple val(meta), path(fai), path(gzi)

GATK4_GETPILEUPSUMMARIES requires a 2-element tuple: tuple val(meta), path(fai)

The subworkflow currently passes the same ch_fai channel to both processes without transformation. If I provide the 3-element tuple required by Mutect2, GETPILEUPSUMMARIES crashes. If I provide the 2-element tuple, MUTECT2 crashes.

Command used and terminal output

Relevant files

// ...
GATK4_MUTECT2(
ch_input,
ch_fasta,
ch_fai, // Expects [meta, fai, gzi]
ch_dict,
// ...
)

// ...

GATK4_GETPILEUPSUMMARIES(
    ch_pileup_input,
    ch_fasta,
    ch_fai, // Expects [meta, fai] -- CONFLICT
    ch_dict,
    // ...
)

System information

No response

Start at the bam_tumor_only_somatic_variant_calling_gatk subworkflow and inspect the GATK4_MUTECT2 and GATK4_GETPILEUPSUMMARIES input definitions. Trace how ch_fai is passed to both modules, then verify that the subworkflow supplies each module with the tuple structure it expects without causing either process to fail.