refined star workflow

dge_workflow/dge_star_template.sh

@@ -105,6 +105,10 @@ mcdir $baseDir/alignments
 
 star_align.kts ${igenome} $(ls ${baseDir}/lanereps_pooled/*.fastq.gz)
 
+dge_bam_correlate . &
+
+mailme "$project: mapping done"
+
 
 ########################################################################################################################
 ### Differential Expression Analysis

dge_workflow/star_align.kts

@@ -127,12 +127,13 @@ evalBash("rm - rf *STARgenome *.Log.progress.out _STARtmp *.SJ.out.tab *Log.out"
 
 // Do reporting and perform bam correlation (but don't wait for the results)
 evalBash("""
-rend.R - e ${'$'}NGS_TOOLS / dge_workflow / star_qc.R.
+rend.R -e ${'$'}NGS_TOOLS/dge_workflow/star_qc.R .
 
 # Condense counts into matrix
 dge_star_counts2matrix
 
 # http://superuser.com/questions/178587/how-do-i-detach-a-process-from-terminal-entirely
-nohup dge_bam_correlate &
-#dge_bam_correlate &
+# disabled since it does not work for functions (see http://stackoverflow.com/questions/16435629/linux-shell-script-call-a-function-by-nohup
+#nohup dge_bam_correlate . &
+#dge_bam_correlate . &
 """)