Added modules for fast assembly using MEGAHIT

rules/Assembly/MGMT.rules

@@ -294,3 +294,90 @@ rule ASSEMBLY_MT_MAPPING:
         # index
         samtools index $PREFIX.sorted.bam
         """
+
+
+################
+# ## MGMT FAST ASSEMBLY USING MEGAHIT
+################
+
+rule ASSEMBLY_MG_FAST_1:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_1.json" % A_OUT
+    input:
+        preprocessed_mg('R1'),
+        preprocessed_mg('R2'),
+        preprocessed_mg('SE'),
+        '{dir}/MT.assembly_1/final.contigs.fa'.format(dir=A_OUT)
+    output:
+        '{dir}/MGMT.assembly_1/final.contigs.fa'.format(dir=A_OUT)
+    params:
+        outdir = "{dir}/MGMT.assembly_1".format(dir=A_OUT)
+    shell:
+        """
+        MAX_READ_LEN=$(cat {input} | sed -n '1~4s/^@/>/p;2~4p' |\
+        awk '$0 ~ \">\" {{c=0\"\t\"; }} $0 !~ \">\" {{c+=length($0); max=(max>c)?max:c;}} END {{print max}}')
+        echo "Max read length: $MAX_READ_LEN"
+        MEMBYTES=$(({MEMTOTAL}*1000*1000*1000))
+        echo "Available memory in bytes: $MEMBYTES"
+        megahit -o {params.outdir} --cpu-only -m $MEMBYTES --mem-flag 1\
+        -l $MAX_READ_LEN --input-cmd "cat {input}" -t {THREADS} --continue > {log} 2>&1
+        """
+
+rule ASSEMBLY_MGMT_EXTRACT_UNMAPPED_FROM_FAST_1:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1.json" % A_OUT
+    input:
+        preprocessed_mg('R1'),
+        preprocessed_mg('R2'),
+        preprocessed_mg('SE'),
+        '{dir}/MGMT.assembly_1/final.contigs.fa'.format(dir=A_OUT),
+        expand('{dir}/MGMT.assembly_1/final.contigs.fa.{ext}', dir=A_OUT, ext=['amb', 'bwt', 'pac', 'sa', 'ann'])
+    output:
+        expand('{dir}/{name}', name=[
+            'MG.R1.unmapped.fq',
+            'MG.R2.unmapped.fq',
+            'MG.SE.unmapped.fq'], dir=A_OUT)
+    shell:
+        """
+        TMP_FILE=$(mktemp --tmpdir={TMPDIR} -t "alignment_XXXXXX.bam")
+        BUFFER=$(mktemp --tmpdir={TMPDIR} -t "alignment_buffer_XXXXXX.bam")
+        bwa mem -v 1 -t {THREADS} {input[3]} {input[0]} {input[1]} | samtools view -@ {THREADS} -bS - > $TMP_FILE
+        samtools merge -@ {THREADS} -u - \
+        <(samtools view -@ {THREADS} -u  -f 4 -F 264 $TMP_FILE) \
+        <(samtools view -@ {THREADS} -u -f 8 -F 260 $TMP_FILE) \
+        <(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]}
+        rm -rf $BUFFER* $TMP_FILE
+        """
+
+rule ASSEMBLY_MGMT_FAST_2:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_2.json" % A_OUT
+    input:
+        expand('{dir}/{name}', name=[
+            'MG.R1.unmapped.fq',
+            'MG.R2.unmapped.fq',
+            'MG.SE.unmapped.fq'], dir=A_OUT)
+    output:
+        '{dir}/MGMT.assembly_2/final.contigs.fa'.format(dir=A_OUT)
+    params:
+        outdir = "{dir}/MGMT.assembly_2".format(dir=A_OUT)
+    shell:
+        """
+        MAX_READ_LEN=$(cat {input} | sed -n '1~4s/^@/>/p;2~4p' | \
+        awk '$0 ~ \">\" {{c=0\"\t\"; }} $0 !~ \">\" {{c+=length($0); max=(max>c)?max:c;}} END {{print max}}')
+        MEMBYTES=$(({MEMTOTAL}*1000*1000*1000))
+        megahit -o {params.outdir} --cpu-only -m $MEMBYTES --mem-flag 1 -l $MAX_READ_LEN \
+        --input-cmd "cat {input}" -t {THREADS} --continue > {log} 2>&1
+        """
+

rules/Assembly/master.rules

@@ -34,3 +34,9 @@ rule ASSEMBLY_MG_ALL:
     shell:
         "echo 'MG Assembly Done'"
 
+#rule ASSEMBLY_FAST:
+#    input:
+#        "%s/MGMT.assembly.merged.fa" % A_OUT
+#    shell:
+#        "echo 'MGMT fast assembly Done'"
+#