Parameter skip_spp has no effect

[lextallan]

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:

Command error:
WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Loading required package: Rcpp
Error in if ((crosscorr$rel.phantom.coeff >= 0) & (crosscorr$rel.phantom.coeff < :
missing value where TRUE/FALSE needed
Calls: source -> withVisible -> eval -> eval
Execution halted

Some googling suggests that perhaps since duplicates have already been removed run_spp_nodups.R should be used instead of run_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]

[ggrimes]

I am having the same issue is there a work around?

[xchan-wcm]

I am also having the same issue.

System information
N E X T F L O W ~ version 22.10.4
Launching https://github.com/nf-core/chipseq DSL2 - revision: 51eba00 [master]

[JoseEspinosa]

The skip_spp parameter is back in the dev branch, you can give it a try in case you are interested.

[tianliu9]

Hi Jose,

I still encountered this error with using this script:

nextflow run nf-core/chipseq
-profile singularity
--input Foreman_lab_ChIPseq.csv
--genome GRCh38
--narrow_peak false
--read_length 150
--macs_gsize 2862089864
--outdir $OUTPUT
--skip_spp
-resume

What should I do to fix this error? Thanks!

[JoseEspinosa]

Hi, you would need to run the dev version of the pipeline adding -r dev to your current nextflow command

[JoseEspinosa]

Fixed in #339