New DSL2 main.nf isn't processing bam files

[kellywuthrich]

I am trying to run the DSL2 main.nf script but keep running into issues with the renaming of files. I believe since I am running just .bam files, none of the renaming conventions are working like for R1/R2. However, I can't figure out how to edit it to ignore any renaming etc. I keep getting ERROR ~ fromIndex = -1 at line ~149-150. Any suggestions?

[bwlang]

can you share the command line you're running? I have an idea to address your issue but I'd like to test with your circumstance.

[kellywuthrich]

Thanks for checking this out. I am testing with just a single bam file named KA11L.bam right now to figure out the code.

nextflow run main.nf
--ubam_dir /home/data/ccox/ubam_test
--genome a-apleto
--genomes /home/data/ccox/references.config
--flowcell KA11L_test
--outputDir em-seq_output

[bwlang]

hmm - I'm not able to reproduce your issue when i make a small single bam file in a directory and run with the same set of arguments (but different genome etc.)

if your files are small enough, can you upload a tar.gz file