Only used fastq's named correctly

CHANGELOG.md

@@ -5,6 +5,9 @@
 * Add memory limit per thread for samtools sort (#108)
 * Remove parsing restrictions for submitted stranded/spike/species (#105, #106)
 * Pass unidentified ends instead of overwriting it as unknown
+* Move fastqc process before trim to catch fastq errors (#107)
+* Only use fastq's that match *.R[1,2].fastq.gz naming convention (#107)
+* Add error output for no fastq's
 
 *Known Bugs*
 * Override params (inputBag, fastq, species) aren't checked for integrity

workflow/rna-seq.nf

@@ -287,7 +287,7 @@ if (fastqsForce != "") {
       fastqs_fastqc
     }
 } else {
-  fastqs.into {
+  fastqs.collect().into {
     fastqs_parseMetadata
     fastqs_fastqc
   }
@@ -304,7 +304,7 @@ process parseMetadata {
     path file from fileMeta
     path experimentSettings, stageAs: "ExperimentSettings.csv" from experimentSettingsMeta
     path experiment from experimentMeta
-    path (fastq) from fastqs_parseMetadata
+    path (fastq) from fastqs_parseMetadata.collect()
     val fastqCount
 
   output:
@@ -376,6 +376,10 @@ process parseMetadata {
     then
       fastqCountError=true
       fastqCountError_details="**Too many fastqs detected (>2)**"
+    elif [ "${fastqCount}" -eq "0" ]
+    then
+      fastqCountError=true
+      fastqCountError_details="**No valid fastqs detected (may not match .R{1,2}.fastq.gz convention)**"
     elif [ "\${endsMeta}" == "se" ] && [ "${fastqCount}" -ne "1" ]
     then
       fastqCountError=true
@@ -486,6 +490,7 @@ fastqError_fl.splitCsv(sep: ",", header: false).separate(
 
 //  Replicate errors for multiple process inputs
 fastqCountError.into {
+  fastqCountError_fastqc
   fastqCountError_trimData
   fastqCountError_getRefInfer
   fastqCountError_downsampleData
@@ -498,7 +503,6 @@ fastqCountError.into {
   fastqCountError_dedupData
   fastqCountError_makeBigWig
   fastqCountError_countData
-  fastqCountError_fastqc
   fastqCountError_dataQC
   fastqCountError_aggrQC
   fastqCountError_uploadQC
@@ -507,6 +511,7 @@ fastqCountError.into {
   fastqCountError_failPreExecutionRun_fastq
 }
 fastqReadError.into {
+  fastqReadError_fastqc
   fastqReadError_trimData
   fastqReadError_getRefInfer
   fastqReadError_downsampleData
@@ -519,7 +524,6 @@ fastqReadError.into {
   fastqReadError_dedupData
   fastqReadError_makeBigWig
   fastqReadError_countData
-  fastqReadError_fastqc
   fastqReadError_dataQC
   fastqReadError_aggrQC
   fastqReadError_uploadQC
@@ -535,12 +539,12 @@ process fastqc {
   tag "${repRID}"
 
   input:
-    path (fastq) from fastqs_fastqc
+    path (fastq) from fastqs_fastqc.collect()
     val fastqCountError_fastqc
     val fastqReadError_fastqc
 
   output:
-    path ("*.fastq.gz", includeInputs:true) into fastqs_trimData
+    path ("*.R{1,2}.fastq.gz", includeInputs:true) into fastqs_trimData
     path ("*_fastqc.zip") into fastqc
     path ("rawReads.csv") into rawReadsInfer_fl
 

workflow/scripts/bdbag_fetch.sh

@@ -18,7 +18,7 @@ if [ "${validate}" != "is valid" ]
 then
     exit 1
 fi
-for i in $(find */ -name "*R*.fastq.gz")
+for i in $(find */ -name "*.R[1-2].fastq.gz")
 do
     path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
     cp ${i} ./${path}