Not able to find "AlignerBoost.jar" on internet .

[arpit20328]

Config file needs the following...path

path_alignerboost: /mnt/ngsnfs/tools/dev/Wochenende/dependencies/AlignerBoost.jar

Can anyone share AlignerBoost.jar file link available for download ?

[colindaven]

Hmm, are you sure you've downloaded and are using the right repo ? Last time we discussed using nf_wochenende, the current version. The older tool -this repo- called wochenende should NOT be used. It has a lot of older features and is difficult to globally install, hence the deprecated tag.

There is no AlignerBoost.jar link here :
https://github.com/MHH-RCUG/nf_wochenende/blob/main/nextflow.config

[colindaven]

Sorry about the confusion !

[arpit20328]

hi @colindaven

actually I am using direct run_Wochenende.py on my Paired end FASTQ files.

and I did not kept any path for alignerboost in the config file..... but it the pipeline ran smoothly,.

so I am guessing that aligner boost is not required for the python file.
I am not using nextflow as of now...

[colindaven]

I see, thanks for the info @arpit20328

So, that way of using it is completely valid of course. We were recommended by the reviewers to package all the tools into Nextflow because of the following advantages.

• ease of cluster submission
• resume functionality
• easy use of multiple different conda envs (containers would be even better)
• because Nextflow and Snakemake are now "standard" in their eyes

So it was packaged into Nextflow, and older config and experiments (AlignerBoost and the functionality for Solid which is an old sequencer type) was removed. That said, the R visualization code was not yet ported into nf_wochenende since an R server was lacking at my current employer, and scripts would need to be extensively rewritten using R singularity containers.

Most of the Wochenende code was written for submission to SLURM. If you use another job scheduler you'd need to manually adapt the scripts. That would be easier using nf_wochenende.

cheers
Colin