DRIMSEQ_FILTER error about rnasplice HOT 5 CLOSED

Upon isolating the run_drimseq_filter.R script in ./bin/ and running it on the specific input files and arguments, it would seem R does not recognize the filtering arguments as numerics, but rather as strings:

run_drimseq_filter.R: Line 27
min_samps_gene_expr <- args[4]
min_samps_feature_expr <- args[5]
min_samps_feature_prop <- args[6]
min_feature_expr <- args[7]
min_feature_prop <- args[8]
min_gene_expr <- args[9]

Thus comparisons later on fail, perhaps force the arguments into numbers will solve the problem. Weirdly enough, when I first installed the rnasplice pipeline and ran the test profile, everything worked.

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I followed the same process, with running run_drimseq_filter.R myself, and when changing the class to numeric does solve the error, and when chancing the class to a character recreates the error "min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE" in the DRIMSeq::dmFilter function.

So the fix should be stating the class to numeric of the args in line 27.

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Hello @DwinGrashof

Casting to numeric definitely seems like the correct fix. Could you also provide your nextflow.log and a snippet of the process which shows the command line which is run for run_drimseq_filter.R

Thanks!

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Hello @DwinGrashof and @bio-info-guy

We have just generated a v1.0.1 release with the patch discussed above. Please give it a try and let us know if it has fixed your issue.

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Dear @jma1991 ,

Patch v1.0.1 seems to have solved the min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE issue as expected.
I am running into another issue with stageR now, but I will post this first on the slack channel, and make a separate issue if necessary.

This issue can be closed, thanks a lot!

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