Potential variable name bug - freemuxlet.nf: grouplist_name

[bednarsky]

Dear hadge team,

thanks for your amazing work, the pipeline seems incredibly useful!

My process to run hadge

I am trying to run it in the genetic mode (reference-free) in multi-sample mode, providing a sample_sheet that matches the example you recently provided. I cloned the repo and run it with this command nextflow run main.nf -c ~/path/to/config -profile cluster.

Note: also this error is shown, but does not kill the pipeline: unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

Potential bug

The pipeline fails with the error:

Caused by: No such variable: grouplist_name -- Check script './modules/././gene_demulti/freemuxlet.nf' at line 71

→ in this file once a variable grouplist_name is used, but above the variable is always called grouplist. I changed it in the source code pipeline source code and it seems to work (until the next error - I will write another issue)

Is this a bug, or is my error coming from something I did wrong?

[wxicu]

hey, thanks for pointing this out. We already noticed this bug and @mari-ga already fix it in her fork. You are totally right. We will try to merge her PR asap.

[bednarsky]

Amazing, thanks for the fast response!

[wxicu]

This is resolved in #20