ERROR ~ No such variable: GRCh37 about chipseq

[tiagochst]

Same problem is profile set to -profile standard,docker.

[tiagochst]

Also just to check. I'm not getting this output from macs, does the tests produce this file?

.bdg bedGraph format files which can be imported to UCSC genome browser or be converted into even smaller bigWig files.

[ewels]

Hi @tiagochst,

I have no idea why you're getting the No such variable error - your command looks fine. I assume you're running the latest version of the code on the dev branch? We'll see if we can replicate it when we get a chance (things are busy here in the run up to summer sorry).

Phil

[tiagochst]

Hi @ewels Yes. I got this with the last version of the master.

Line 104 is: params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false

This is the log file.

[tiagochst]

If I print params.genome and params.genomes before line 104 I got.

genome = GRCh37, genomes = false

[tiagochst]

So comparing the rna-seq github, it is missing to add this line in the chipseq config:
https://github.com/nf-core/rnaseq/blob/master/nextflow.config#L44

[tiagochst]

This will solve the problem, but the profile will still have to be -profile standard,docker

[ewels]

Not yet resolved...

[bc2zb]

So I think I figured this out. If your HPC has igenomes available on your system, update the igenomes.config file to reflect that base directory, and include it in your profile. I also tried adding my own bwa index and gtf file, but for whatever reason, that doesn't work. Should I submit that as another issue, or add it here?

[apeltzer]

Add another issue then - that shouldn't be the case. Include some sample call so we can try to reproduce the issue :-)

[chuan-wang]

Issue solved by declaring params.genome in main.nf (PR #38 ).