Add catch for no reads being left after fastp filtering (#74)

artic-network · Oct 18, 2024 · adc958d · adc958d
1 parent 0f4a158
commit adc958d
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Showing 3 changed files with 11 additions and 4 deletions.
diff --git a/docs/errorcodes.txt b/docs/errorcodes.txt
@@ -7,4 +7,5 @@
 6   Spike in not understood/not in reference JSON
 7   No output files for one half of a read-pair
 8   Mismatching paired read FASTQ headers
-9   Kraken report formatting error
+9   Kraken report formatting error
+10  No reads left after fastp, either no reads passed filtering or read files are misformatted
diff --git a/modules/preprocess.nf b/modules/preprocess.nf
@@ -6,7 +6,7 @@ process fastp_paired {
 
     container "${params.wf.container}:${params.wf.container_version}"
 
-    errorStrategy {task.exitStatus == 255 ? "ignore" : "terminate"}
+    errorStrategy {task.exitStatus in [255, 10] ? "ignore" : "terminate"}
 
     input:
         val unique_id
@@ -31,10 +31,14 @@ process fastp_paired {
 
     if [ -s ${unique_id}_1.fastp.fastq ]; then
         bgzip --threads $task.cpus -c ${unique_id}_1.fastp.fastq > ${unique_id}_1.fastp.fastq.gz
+    else
+        exit 10
     fi
 
     if [ -s ${unique_id}_2.fastp.fastq ]; then
         bgzip --threads $task.cpus -c ${unique_id}_2.fastp.fastq > ${unique_id}_2.fastp.fastq.gz
+    else
+        exit 10
     fi    
     """
 
@@ -48,7 +52,7 @@ process fastp_single {
 
     container "${params.wf.container}:${params.wf.container_version}"
 
-    errorStrategy {task.exitStatus == 255 ? "ignore" : "terminate"}
+    errorStrategy {task.exitStatus in [255, 10] ? "ignore" : "terminate"}
 
     input:
         val unique_id
@@ -73,6 +77,8 @@ process fastp_single {
 
     if [ -s ${unique_id}.fastp.fastq ]; then
         bgzip --threads $task.cpus -c ${unique_id}.fastp.fastq > ${unique_id}.fastp.fastq.gz
+    else
+        exit 10
     fi
     """
 }

diff --git a/nextflow.config b/nextflow.config
@@ -32,7 +32,7 @@ manifest {
     description     = 'Classify metagenomic sequence data from human respiratory infections.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v1.3.1'
+    version         = 'v1.3.2'
 }
 
 profiles {