From 3ad4a0cb0b38bc59c58df644c1b36c17bc1828c9 Mon Sep 17 00:00:00 2001
From: cgpu <chatzipantsiou@gmail.com>
Date: Wed, 4 Dec 2019 01:23:29 +0000
Subject: [PATCH] Addresses https://github.com/cgpu/sarek/issues/3 ; Known
 issue with bwa | smatools pipe

---
 main.nf | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/main.nf b/main.nf
index 6cfaf82ebf..a0f912619b 100644
--- a/main.nf
+++ b/main.nf
@@ -675,9 +675,16 @@ process MapReads {
     convertToFastq = hasExtension(inputFile1, "bam") ? "gatk --java-options -Xmx${task.memory.toGiga()}g SamToFastq --INPUT=${inputFile1} --FASTQ=/dev/stdout --INTERLEAVE=true --NON_PF=true | \\" : ""
     input = hasExtension(inputFile1, "bam") ? "-p /dev/stdin - 2> >(tee ${inputFile1}.bwa.stderr.log >&2)" : "${inputFile1} ${inputFile2}"
     """
-        ${convertToFastq}
-        bwa mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} \
-        ${input} |  samtools sort - > ${idSample}_${idRun}.bam
+    # map to sam
+    ${convertToFastq}
+    bwa mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} \
+    ${input} >  ${idSample}_${idRun}.sam
+
+    # create bam
+    samtools view -@ ${task.cpus} -b -h -O BAM -o ${idSample}_${idRun}.bwamem.bam ${idSample}_${idRun}.sam
+
+    # sort bam
+    samtools sort -@ ${task.cpus} -o ${idSample}_${idRun}.bam
     """
 }