From 792dbe387353ac551a0a8ee1b33e318ff361303a Mon Sep 17 00:00:00 2001
From: Shaman <shaman.narayanasamy@uni.lu>
Date: Tue, 31 Mar 2015 14:37:39 +0200
Subject: [PATCH] Comment out Trinity

---
 rules/Assembly/MGMT.rules | 206 +++++++++++++++++++-------------------
 rules/Util.rules          |   5 +-
 2 files changed, 106 insertions(+), 105 deletions(-)

diff --git a/rules/Assembly/MGMT.rules b/rules/Assembly/MGMT.rules
index 7e97db8..5543f38 100644
--- a/rules/Assembly/MGMT.rules
+++ b/rules/Assembly/MGMT.rules
@@ -10,7 +10,7 @@ rule ASSEMBLY_MT_MEGAHIT_1:
     log:
         A_LOG
     benchmark:
-        "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_1.json" % A_OUT
+        "%s/benchmarks/ASSEMBLY_MT_MEGAHIT_1.json" % A_OUT
     input:
         preprocessed_mt('R1'),
         preprocessed_mt('R2'),
@@ -35,7 +35,7 @@ rule ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_MEGAHIT_1:
     log:
         A_LOG
     benchmark:
-        "%s/benchmarks/ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_ASSEMBLY_1.json" % A_OUT
+        "%s/benchmarks/ASSEMBLY_MT_EXTRACT_UNMAPPED_FROM_MEGAHIT_1.json" % A_OUT
     input:
         preprocessed_mt('R1'),
         preprocessed_mt('R2'),
@@ -68,7 +68,7 @@ rule ASSEMBLY_MT_MEGAHIT_2:
     log:
         A_LOG
     benchmark:
-        "%s/benchmarks/ASSEMBLY_MT_ASSEMBLY_2.json" % A_OUT
+        "%s/benchmarks/ASSEMBLY_MT_MEGAHIT_2.json" % A_OUT
     input:
         expand('{dir}/{name}', name=[
             'MT.R1.unmapped.fq',
@@ -91,7 +91,7 @@ rule ASSEMBLY_MT_CAT_MEGAHIT:
     log:
         A_LOG
     benchmark:
-        "%s/benchmarks/ASSEMBLY_MT_CAT_ASSEMBLY.json" % A_OUT
+        "%s/benchmarks/ASSEMBLY_MT_CAT_MEGAHIT.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)
@@ -104,105 +104,105 @@ rule ASSEMBLY_MT_CAT_MEGAHIT:
 #########################
 ## ## MT TRINITY 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}
-        """
-
+#
+#rule ASSEMBLY_MT_TRINITY_TRINITY_1:
+#    log:
+#        A_LOG
+#    benchmark:
+#        "%s/benchmarks/ASSEMBLY_MT_TRINITY_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_TRINITY_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_TRINITY_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_TRINITY.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/Util.rules b/rules/Util.rules
index fcf78ca..aea13ba 100644
--- a/rules/Util.rules
+++ b/rules/Util.rules
@@ -157,11 +157,11 @@ rule INDEX_FASTA_FILE:
         bwa index {wildcards.fasta} > {log} 2>&1
         """
 
-rule CHECK_TOOLS_VERSION:
+rule CHECK_TOOL_VERSION:
     log:
         U_LOG
     benchmark:
-        "%s/benchmarks/CHECK_TOOLS_VERSION.json" % U_OUT
+        "%s/benchmarks/CHECK_TOOL_VERSION.json" % U_OUT
     output:
         "%s/tools.versions" % U_OUT
     shell:
@@ -191,6 +191,7 @@ rule CHECK_TOOLS_VERSION:
         echo "# cap3"  >> {output}
         echo "# coverageBed"  >> {output}
         echo "# bh_tsne" >> {output}
+        echo "# KronaTools" >> {output}
 
         """
 
-- 
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