nf-core/chipseq blacklist error about chipseq

[drpatelh]

Hi @mglgc . A similar issue propped up with the atacseq pipeline yesterday.
nf-core/atacseq#39

Error message: (No such file or directory). Exiting! generally means its a file permission issue.

Can you send me the command you are using? and check if the blacklist file exists in the pulled version of the pipeline?
ls ~/.nextflow/assets/nf-core/chipseq/assets/blacklists/GRCh37-blacklist.bed

[mglgc]

Hi drpatelh,
Thanks for your reply.
I don't think about any permission issue as I've just said I've alternatively used the --blacklist option with my own path and blacklist file. Anyway, yo'll find below the relevant command options I'm using:

nextflow run nf-core/chipseq --genome GRCh37 --aligner hisat2 --singleEnd -profile docker

Best!

[drpatelh]

Ok. So --aligner hisat2 is definitely not an option for the chipseq pipeline because it only uses bwa mem. Thats from the rnaseq pipeline! Shouldnt be the cause of the error though...

You also need to give the pipeline a design.csv which is a mandatory argument:
https://github.com/nf-core/chipseq/blob/master/docs/usage.md#running-the-pipeline

Can you join the chipseq channel on the nf-core Slack workspace and we can debug further if required.
https://nf-core-invite.herokuapp.com/

[mglgc]

Dear drpatelh,
Of course I have a design.csv. Bear in mind that I have only one error, that related to the blacklist not found file. Regarding the hisat2 aligner, I have used it in several chipseq pipeline runnings with no problem.
I'll join by Slack to report the error. Thanks.