When running a BAM input, ARRIBA_VISUALISATION and FUSIONINSPECTOR modules do not run

[preethabalakrishnan]

Description of the bug

Thank you so much for putting together this pipeline with many fusion tools to choose from. I tested this pipeline with one publicly available sample and it worked well with FASTQ files. In this case, ARRIBA_VISUALISATION and FUSIONINSPECTOR worked and I got good representations for the reported fusions. Now, I tested the pipeline with BAM output files from the same run where as required I also provided the chimeric junctions .junction file and the splice junction .SJ.out.tab file. The pipeline runs through without any error but I do not get any visualization in this case (see attached screenshot)

. In case of FUSIONINSPECTOR, it takes only a FASTQ as input (see here). Maybe this can be updated such that it takes even a BAM file as input and provides visualization?

In case of ARRIBA_VISUALISATION , I am not exactly sure why it did not run. Ideally, it should have worked.

I am new here and any suggestion is welcome :)

Command used and terminal output

nextflow run main.nf -profile docker --tools arriba,starfusion,fusionreport,fusioninspector --input samplesheet_bam.csv --genomes_base ./references --outdir output_bam_with_genelist -c nextflow.config --no_cosmic

Relevant files

samplesheet_bam.csv

System information

Nextflow version 25.10.0

[rannick]

ARRIBA_VISUALISATION depends on FUSIONINSPECTOR. Indeed FusionInspector needs fastq files and does not take in bam files. what we could do is implement a bam to fastq step, but that might defeat the purpose. @nvnieuwk looping you in as you implemented the bam files

[preethabalakrishnan]

Thank you for replying so fast :) For now, the best is to convert it to a FASTQ file and continue I guess. It would be great if we have visualizations in case of a BAM input just like in case of a FASTQ

[nvnieuwk]

Yes I made a conscious decision here to not convert the BAM files to FASTQ as this would defeat the point IMO. However, we might add a warning or error for this specific case to inform the user better. Or add the conversion step if you think it makes sense in this case