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Parameter skip_spp has no effect #311
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I am having the same issue is there a work around? |
I am also having the same issue. System information |
The |
Hi Jose, I still encountered this error with using this script: nextflow run nf-core/chipseq What should I do to fix this error? Thanks! |
Hi, you would need to run the |
Fixed in #339 |
Description of the bug
Hi!
It appears the ability to skip phantompeakqualtools has been left out. "skip_spp" is listed in the parameters on the nf-core site but there's no inclusion of the parameter in the workflow to make the module skippable (i.e processes PHANTOMPEAKQUALTOOLS and MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS should be within
if (!params.skip_spp) { }
). Just double checked and indeed even running the test profile with option --skip_spp still shows phantompeakqualtools being run.As another issue, I've repeatedly had issues with phantompeakqualtools (including in previous nf-core pipelines) with something akin to the following error:
Some googling suggests that perhaps since duplicates have already been removed
run_spp_nodups.R
should be used instead ofrun_spp.R
. The test data still runs fine though so maybe it's just a problem with my datasets?Thanks!
Command used and terminal output
nextflow run nf-core/chipseq -r 2.0.0 -profile test,singularity --skip_spp
Relevant files
No response
System information
N E X T F L O W ~ version 22.04.0
Launching
https://github.com/nf-core/chipseq
DSL2 - revision: 51eba00 [2.0.0]The text was updated successfully, but these errors were encountered: