fix: throw error if trimmed fastq files are (nearly) empty

CCBR · Nov 22, 2024 · a08b4e4 · a08b4e4
1 parent 4d42da4
commit a08b4e4
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diff --git a/tests/data/fastq/WT_S1.R1.trunc.fastq.gz b/tests/data/fastq/WT_S1.R1.trunc.fastq.gz
diff --git a/tests/data/fastq/WT_S1.R2.trunc.fastq.gz b/tests/data/fastq/WT_S1.R2.trunc.fastq.gz
diff --git a/workflow/rules/paired-end.smk b/workflow/rules/paired-end.smk
@@ -96,9 +96,18 @@ rule trim_pe:
         -m {params.minlen}:{params.minlen} \
         -b file:{params.fastawithadaptersetd} -B file:{params.fastawithadaptersetd} \
         -j {threads} -o {output.out1} -p {output.out2} {input.file1} {input.file2}
+    for f in {output.out1} {output.out2}; do
+        check_output=$(gzip -cd $f | head | wc -l)
+        if [ $check_output -lt 10 ]; then
+            echo "ERROR: Trimmed FastQ file is empty. $f"
+            exit 1
+        fi
+    done
     """
 
 
+
+
 rule fastqc:
     """
     Quality-control step to assess sequencing quality of the raw data after removing

diff --git a/workflow/rules/single-end.smk b/workflow/rules/single-end.smk
@@ -88,6 +88,11 @@ if config['options']['small_rna']:
             -n 5 -O 5 -q {params.leadingquality},{params.trailingquality} \
             -m 16 -b file:{params.fastawithadaptersetd} -j {threads} \
             -o {output.outfq} {input.infq}
+        check_output=$(gzip -cd {output.outfq} | head | wc -l)
+        if [ $check_output -lt 10 ]; then
+            echo "ERROR: Trimmed FastQ file is empty."
+            exit 1
+        fi
         """
 else:
     # Use default trimming rule for long RNAs
@@ -120,6 +125,11 @@ else:
             -n 5 -O 5 -q {params.leadingquality},{params.trailingquality} \
             -m {params.minlen} -b file:{params.fastawithadaptersetd} -j {threads} \
             -o {output.outfq} {input.infq}
+        check_output=$(gzip -cd {output.outfq} | head | wc -l)
+        if [ $check_output -lt 10 ]; then
+            echo "ERROR: Trimmed FastQ file is empty."
+            exit 1
+        fi
         """