Merge branch 'dea.RFix' into 'master'

Corrected issue where a gene with 0 read counts could crash the dea.R scripts.

See merge request !3

nextflow.config

 process.executor='slurm'
 process.queue='128GB,256GB,256GBv1'
 process.clusterOptions = '--hold'
-trace.enabled = true
+trace.enabled = false
 trace.file = 'pipeline_trace.txt'
 trace.field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'

process_scripts @ 291e1c35

-Subproject commit 0bdf56d5bdb9252ce418fcf7d0c7bdbcee9ff4a1
+Subproject commit 291e1c352873ce14881ab8b1822fa7d3183b946b

workflow/scripts/dea.R

@@ -94,6 +94,7 @@ for (i in 1:a) {
       filt.out <- na.omit(output[output$fdr < 0.05,])
       if (nrow(filt.out) > 2) {
       	 subset <- logcpm[row.names(logcpm) %in% filt.out$symbol,]
+	 subset <- subset[!apply(subset, 1, function(x) {any(x == 0)}),]
       	 gnames <- filt.out[c('ensembl','symbol')]
       	 s <- merge(gnames,subset,by.x="ensembl",by.y="row.names",all.x=FALSE,all.y=TRUE,sort=FALSE)
       	 STREE <- hclust(dist(t(subset)))
@@ -148,6 +149,7 @@ for (i in 1:a) {
       filt.out <- na.omit(output[output$fdr < 0.05,])
       if (nrow(filt.out) > 2) {
       subset <- logcpm[row.names(logcpm) %in% filt.out$symbol,]
+      subset <- subset[!apply(subset, 1, function(x) {any(x == 0)}),]
       gnames <- filt.out[c('ensembl','symbol')]
       s <- merge(gnames,subset,by.x="ensembl",by.y="row.names",all.x=FALSE,all.y=TRUE,sort=FALSE)
       STREE <- hclust(dist(t(subset)))