8000 Specify pScreenAdjusted argument depending on analysis method by jma1991 · Pull Request #113 · nf-core/rnasplice · GitHub
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Specify pScreenAdjusted argument depending on analysis method #113

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Merged
merged 3 commits into from
Jan 8, 2024
Merged

Specify pScreenAdjusted argument depending on analysis method #113

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8043897
Specify pScreenAdjusted argument depending on analysis method
jma1991 Jan 8, 2024
f0dd323
Strip version using regex
jma1991 Jan 8, 2024
fcf8a8d
Temp check of docker settings
jma1991 Jan 8, 2024
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4 changes: 2 additions & 2 deletions bin/run_stager.R
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ library(stageR)

stripVersion <- function(x) {

substr(x, 1, 15)
sub("\\..*", "", x)

}

Expand Down Expand Up @@ -148,7 +148,7 @@ object <- stageRTx(
pScreen = output[["pScreen"]],
pConfirmation = output[["pConfirmation"]],
tx2gene = output[["tx2gene"]],
pScreenAdjusted = FALSE
pScreenAdjusted = switch(analysis, "dexseq" = TRUE, "drimseq" = FALSE)
)


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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -218,13 +218,13 @@ profiles {
}
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
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0