Fix for issue #87

rules/Assembly/hybrid/extract-unmapped.rules

@@ -8,9 +8,17 @@ samtools merge -@ {THREADS} -u - \
 <(samtools view -@ {THREADS} -u -f 12 -F 256 $TMP_FILE) | \
 samtools view -@ {THREADS} -bF 0x800 -  | samtools sort -o -@ {THREADS} -m {MEMCORE}G -n - $BUFFER | \
 bamToFastq -i stdin -fq {output[0]} -fq2 {output[1]}
-bwa mem -v 1 -t {THREADS} {input[3]} {input[2]} | \
-samtools view -@ {THREADS} -bS - | samtools view -@ {THREADS} -uf 4 - | \
-bamToFastq -i stdin -fq {output[2]}
+
+if [[ -s {input[2]} ]]
+then
+    bwa mem -v 1 -t {THREADS} {input[3]} {input[2]} | \
+    samtools view -@ {THREADS} -bS - | samtools view -@ {THREADS} -uf 4 - | \
+    bamToFastq -i stdin -fq {output[2]}
+else
+    echo "There are no singletons reads. {input[2]} is empty. Generating empty {output[2]}" 
+    touch {output[2]}
+fi
+
 rm -rf $BUFFER* $TMP_FILE
 """
 
@@ -32,26 +40,6 @@ rule extract_unmapped_from_megahit:
     shell:
         EXTRACT_UNMAPPED_SHELL
 
-
-#
-# rule extract_mg_unmapped_from_idba:
-#     input:
-#         'Preprocessing/mg.r1.preprocessed.fq',
-#         'Preprocessing/mg.r2.preprocessed.fq',
-#         'Preprocessing/mg.se.preprocessed.fq',
-#         'Assembly/mg.idba_preprocessed.1.fa',
-#         'Assembly/mg.idba_preprocessed.1.fa.amb',
-#         'Assembly/mg.idba_preprocessed.1.fa.bwt',
-#         'Assembly/mg.idba_preprocessed.1.fa.pac',
-#         'Assembly/mg.idba_preprocessed.1.fa.sa',
-#         'Assembly/mg.idba_preprocessed.1.fa.ann'
-#     output:
-#         'Assembly/mg.r1.unmapped.fq',
-#         'Assembly/mg.r2.unmapped.fq',
-#         'Assembly/mg.se.unmapped.fq'
-#     shell:
-#         EXTRACT_UNMAPPED_SHELL
-
 rule extract_unmapped_from_hybrid_assembly:
     input:
         'Preprocessing/{type}.r1.preprocessed.fq',

rules/Assembly/single-omic/extract-unmapped.rules

@@ -8,9 +8,17 @@ samtools merge -@ {THREADS} -u - \
 <(samtools view -@ {THREADS} -u -f 12 -F 256 $TMP_FILE) | \
 samtools view -@ {THREADS} -bF 0x800 -  | samtools sort -o -@ {THREADS} -m {MEMCORE}G -n - $BUFFER | \
 bamToFastq -i stdin -fq {output[0]} -fq2 {output[1]}
-bwa mem -v 1 -t {THREADS} {input[3]} {input[2]} | \
-samtools view -@ {THREADS} -bS - | samtools view -@ {THREADS} -uf 4 - | \
-bamToFastq -i stdin -fq {output[2]}
+
+if [[ -s {input[2]} ]]
+then
+    bwa mem -v 1 -t {THREADS} {input[3]} {input[2]} | \
+    samtools view -@ {THREADS} -bS - | samtools view -@ {THREADS} -uf 4 - | \
+    bamToFastq -i stdin -fq {output[2]}
+else
+    echo "There are no singletons reads. {input[2]} is empty. Generating empty {output[2]}" 
+    touch {output[2]}
+fi
+
 rm -rf $BUFFER* $TMP_FILE
 """