Targeted pipeline does not work with BWA

[npatel-ah]

Description of the bug

Hello,

I was trying to the V2.0.0 using Docker with --aligner bwa, however, I am getting error.

nextflow run nf-core/crisprseq -profile docker --overrepresented --input samplesheet.csv --analysis targeted --outdir $PWD --aligner bwa -r 2.0.0 -resume

Command used and terminal output

nextflow run nf-core/crisprseq -profile docker  --overrepresented --input samplesheet.csv --analysis targeted --outdir $PWD -aligner bwa  -r 2.0.0 -resume


ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_TARGETED:BWA_INDEX (7)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

[mirpedrol]

Hello @npatel-ah,
this is fixed now in the dev version. If you would like to test it previous to the next release, you can use -r dev with your command. But please note that this version will change while we continue developing.
Thanks for reporting the bug!

[npatel-ah]

Thanks for quick fix and all your support, I am getting error with dev but I understand it's work in progress. I will wait for the new version release, meanwhile I have plenty review.

Project nf-core/crisprseq contains uncommitted changes -- Cannot switch to revision: dev

Thanks