require existence of fastq inputs

dge_workflow/star_align.kts

@@ -50,8 +50,8 @@ if (evalBash("which STAR").exitCode != 0) throw IllegalArgumentException("STAR a
 System.getenv("NGS_TOOLS").let {
     require(it.isNotBlank() && File(it).isDirectory) { "NGS_TOOLS is not defined but needed to locate star_qc.R" }
 }
-require(evalBash("type dge_star_counts2matrix").exitCode==0) {"dge_star_counts2matrix is missing"}
-require(evalBash("type dge_bam_correlate").exitCode==0){"dge_bam_correlate is missing"}
+require(evalBash("type dge_star_counts2matrix").exitCode == 0) { "dge_star_counts2matrix is missing" }
+require(evalBash("type dge_bam_correlate").exitCode == 0) { "dge_bam_correlate is missing" }
 
 
 println("validating inputs...")
@@ -65,12 +65,14 @@ if (!File("${star_index}/SA").isFile())
 //   dge_create_star_index ${igenome}'
 
 
+// make sure all fastq files do exist
+fastqFiles.filter { !it.isFile }.let {
+    require(it.isEmpty()) { "Some fastq files do not exist  ${it.map { it.absoluteFile }.joinToString(", ")}" }
+}
+
 println("running STAR using igenome '${igenome}' for the following files")
 
 val jl = JobList(".starjobs")
-//rm .starjobs
-
-//fastqFiles=$(ls $baseDir/treps_pooled/*fastq.gz)
 
 for (fastqFile in fastqFiles) {
     println("submitting STAR job for $fastqFile")
@@ -118,7 +120,8 @@ joblist.`package$`.`MODULE$`.ImplJobListUtils(jl).createHtmlReport()
 
 
 // cleanup
-evalBash("""rm - rf * STARgenome * .Log.progress.out _STARtmp * .SJ.out.tab *Log.out""")
+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("""

dge_workflow/testdata/featcounts_deseq/test_star.sh

@@ -10,6 +10,6 @@ source $NGS_TOOLS/dge_workflow/dge_utils.sh
 
 #git clone https://github.com/holgerbrandl/kutils && cd kutils && gradle install && cd .. && rm -rf kutils
 
-star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 ~/test.fastq
+star_align.kts /local2/igenomes/Mus_Musculus/Ensembl/GRCm38 ~/mouse_test.fastq.gz
 
 mailme "star test done"
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