[dev] ./genome/genome.fa link not created in output dir

[darked89]

Hello,

I have run:

nextflow run . -profile test,singularity --outdir ../out_test_nf_chipseq

While loading IGV session session:

cd ../out_test_nf_chipseq/igv/broadPeak/
igv.sh
#Loading:
igv_session.xml

IGV reported:

Error loading session session: Cannot locate genome: /full/path/to/out_test_nf_chipseq/genome/genome.fa

I have found ( in one of the subdir in ./work) and soft-linked the genome.fa to out_test_nf_chipseq/genome/genome.fa
after which IGV displayed the results as expected.

This is a fairly minor nuisance, but IMHO it should be addressed.

Many thanks for creating and maintaining such complex pipeline.

Darek Kedra

[JoseEspinosa]

Thanks for reporting @darked89, we should address it before releasing 2.0!

[JoseEspinosa]

Fixed in #279. I close this issue now but let us know if you find any other issue @darked89 Thanks!