From 61d977b241140b1c09e74c09b1cca55f632f3f11 Mon Sep 17 00:00:00 2001
From: Shaman <shaman.narayanasamy@uni.lu>
Date: Fri, 27 Mar 2015 17:36:46 +0100
Subject: [PATCH] Add Trinity MT assembly module. Commented out at the moment
---
rules/Assembly/MGMT.rules | 121 +++++++++++++++++++++++++++++++++---
rules/Assembly/master.rules | 6 +-
2 files changed, 117 insertions(+), 10 deletions(-)
diff --git a/rules/Assembly/MGMT.rules b/rules/Assembly/MGMT.rules
index 26d2c21..58c5633 100644
--- a/rules/Assembly/MGMT.rules
+++ b/rules/Assembly/MGMT.rules
@@ -1,8 +1,12 @@
-################
-# ## MT SECTION
-################
+###################################################################################################
+# MT ASSEEMBLY SECTION
+###################################################################################################
-rule ASSEMBLY_MT_ASSEMBLY_1:
+#########################
+## ## MT MEGAHIT ASSEMBLY
+#########################
+
+rule ASSEMBLY_MT_MEGAHIT_1:
log:
A_LOG
benchmark:
@@ -27,7 +31,7 @@ rule ASSEMBLY_MT_ASSEMBLY_1:
"""
-rule ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1:
+rule ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_MEGAHIT_1:
log:
A_LOG
benchmark:
@@ -60,7 +64,7 @@ rule ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1:
rm -rf $BUFFER* $TMP_FILE
"""
-rule ASSEMBLY_MT_ASSEMBLY_2:
+rule ASSEMBLY_MT_MEGAHIT_2:
log:
A_LOG
benchmark:
@@ -83,7 +87,7 @@ rule ASSEMBLY_MT_ASSEMBLY_2:
--input-cmd "cat {input}" -t {THREADS} --continue > {log} 2>&1
"""
-rule ASSEMBLY_MT_CAT_ASSEMBLY:
+rule ASSEMBLY_MT_CAT_MEGAHIT:
log:
A_LOG
benchmark:
@@ -97,6 +101,109 @@ rule ASSEMBLY_MT_CAT_ASSEMBLY:
"""
cat {input[0]} {input[1]} | awk '/^>/{{print ">contig_MT_" ++i; next}}{{print}}' > {output}
"""
+
+#########################
+## ## MT MEGAHIT ASSEMBLY
+#########################
+#
+#rule ASSEMBLY_MT_ASSEMBLY_TRINITY_1:
+# log:
+# A_LOG
+# benchmark:
+# "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_1.json" % A_OUT
+# input:
+# preprocessed_mt('R1'),
+# preprocessed_mt('R2'),
+# preprocessed_mt('SE')
+# output:
+# '{dir}/MT.assembly_1/final.contigs.fa'.format(dir=A_OUT)
+# params:
+# outdir = "{dir}/MT.assembly_1".format(dir=A_OUT)
+# shell:
+# """
+# Trinity --seqType fq\
+# --left {input[0]} --right {input[1]} --single {input[2]}\
+# --output {output[0]}\
+# --JM {MEMTOTAL}G --CPU {THREADS}\
+# --inchworm_cpu {THREADS} --bflyHeapSpaceMax {MEMTOTAL}G\
+# --bflyCPU {THREADS} --bflyCalculateCPU\
+# --normalize_max_read_cov 25 --full_cleanup\
+# """
+#
+#
+#rule ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_TRINITY_1:
+# log:
+# A_LOG
+# benchmark:
+# "%s/benchmarks/ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1.json" % A_OUT
+# input:
+# preprocessed_mt('R1'),
+# preprocessed_mt('R2'),
+# preprocessed_mt('SE'),
+# '{dir}/MT.assembly_1/final.contigs.fa'.format(dir=A_OUT),
+# expand('{dir}/MT.assembly_1/final.contigs.fa.{ext}', dir=A_OUT, ext=['amb', 'bwt', 'pac', 'sa', 'ann'])
+# output:
+# expand('{dir}/{name}', name=[
+# 'MT.R1.unmapped.fq',
+# 'MT.R2.unmapped.fq',
+# 'MT.SE.unmapped.fq'], dir=A_OUT)
+# shell:
+# """
+# TMP_FILE=$(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_MT_TRINITY_2:
+# log:
+# A_LOG
+# benchmark:
+# "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_2.json" % A_OUT
+# input:
+# expand('{dir}/{name}', name=[
+# 'MT.R1.unmapped.fq',
+# 'MT.R2.unmapped.fq',
+# 'MT.SE.unmapped.fq'], dir=A_OUT)
+# output:
+# '{dir}/MT.assembly_2/final.contigs.fa'.format(dir=A_OUT)
+# params:
+# outdir = "{dir}/MT.assembly_2".format(dir=A_OUT)
+# shell:
+# """
+# Trinity --seqType fq\
+# --left {input[0]} --right {input[1]} --single {input[2]}\
+# --output {output[0]}\
+# --JM {MEMTOTAL}G --CPU {THREADS}\
+# --inchworm_cpu {THREADS} --bflyHeapSpaceMax {MEMTOTAL}G\
+# --bflyCPU {THREADS} --bflyCalculateCPU\
+# --normalize_max_read_cov 25 --full_cleanup\
+# """
+#
+#rule ASSEMBLY_MT_CAT_TRINITY:
+# log:
+# A_LOG
+# benchmark:
+# "%s/benchmarks/ASSEMBLY_MT_CAT_ASSEMBLY.json" % A_OUT
+# input:
+# '{dir}/MT.assembly_1/final.contigs.fa'.format(dir=A_OUT),
+# '{dir}/MT.assembly_2/final.contigs.fa'.format(dir=A_OUT)
+# output:
+# '{dir}/MT.assembly.cat.fa'.format(dir=A_OUT)
+# shell:
+# """
+# cat {input[0]} {input[1]} | awk '/^>/{{print ">contig_MT_" ++i; next}}{{print}}' > {output}
+# """
+##
##################
# ## MGMT SECTION - ASSEMBLY
##################
diff --git a/rules/Assembly/master.rules b/rules/Assembly/master.rules
index 69a28ff..ff8298f 100644
--- a/rules/Assembly/master.rules
+++ b/rules/Assembly/master.rules
@@ -34,9 +34,9 @@ rule ASSEMBLY_MG_ALL:
shell:
"echo 'MG Assembly Done'"
-#rule ASSEMBLY_FAST:
+#rule ASSEMBLY_MG_FAST:
# input:
-# "%s/MGMT.assembly.merged.fa" % A_OUT
+# "%s/MG.assembly.merged.fa" % A_OUT
# shell:
-# "echo 'MGMT fast assembly Done'"
+# "echo 'MG fast assembly done'"
#
--
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