Merge branch 'master' of...

Merge branch 'master' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP into version1.2.1

IMP

@@ -33,7 +33,7 @@ Options:
   --norm            Don't delete the container after use. Useful for debugging.
   --ask             Ask to create directory if it doesn't exist.
   --current         Use the current version of the IMP codebase (what you have pulled).
-  -c CONFIG         Pass a user defined config file. Default: conf/userconfig.imp.json
+  -c CONFIG         Pass a user defined config file. [default: conf/userconfig.imp.json]
   -h --help         Show this help and exit
   -m MG             Path to the metagenomics paired files (must be 2 files).
   -t MT             Path to the metatranscriptomic paired files (2 files).

rules/Assembly/mg.idba.rules

+rule ASSEMBLY_MG_ASSEMBLY_1:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MG_ASSEMBLY_1.json" % A_OUT
+    input:
+        '%s/MG.R1.preprocessed.fq' % P_OUT,
+        '%s/MG.R2.preprocessed.fq' % P_OUT,
+        '%s/MG.SE.preprocessed.fq' % P_OUT,
+    output:
+        '{dir}/MG.assembly_1.fa'.format(dir=A_OUT),
+    shell:
+        """
+        TMPD=$(mktemp -d -t --tmpdir={TMPDIR} "XXXXXX")
+        fq2fa --merge {input[0]} {input[1]} $TMPD/merged.fa
+        fq2fa {input[2]} $TMPD/se.fa
+        echo $TMPDIR
+        idba_ud -r $TMPD/merged.fa \
+        -l $TMPD/se.fa -o $TMPD \
+        --mink {config[idba_ud][mink]} --maxk {config[idba_ud][maxk]} \
+        --step {config[idba_ud][step]} --num_threads {THREADS} \
+        --similar {config[idba_ud][perid]} --pre_correction
+        mv $TMPD/contig.fa {output}
+        """
+        #rm -rf $TMPD
+
+rule ASSEMBLY_MG_EXTRACT_UNMAPPED:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MG_EXTRACT_UNMAPPED.json" % A_OUT
+    input:
+        '%s/MG.R1.preprocessed.fq' % P_OUT,
+        '%s/MG.R2.preprocessed.fq' % P_OUT,
+        '%s/MG.SE.preprocessed.fq' % P_OUT,
+        '{dir}/MG.assembly_1.fa'.format(dir=A_OUT),
+        expand('{dir}/MG.assembly_1.fa.{ext}', dir=A_OUT, ext=['amb', 'bwt', 'pac', 'sa', 'ann'])
+    output:
+        expand('{dir}/{name}', name=[
+            'MG.assembly_1_MG_unmapped.R1.fq',
+            'MG.assembly_1_MG_unmapped.R2.fq',
+            'MG.assembly_1_MG_unmapped.SE.fq'], dir=A_OUT)
+    shell:
+        """
+        TMP_FILE=$(mktemp --tmpdir={TMPDIR} -t "alignment_XXXXXX.bam")
+        BUFFER=$(mktemp --tmpdir={TMPDIR} -t "alignment_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* $TMP_FILE
+        """
+
+rule ASSEMBLY_MG_ASSEMBLY_2:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MG_ASSEMBLY_2.json" % A_OUT
+    input:
+        expand('{dir}/{name}', name=[
+            'MG.assembly_1_unmapped.R1.fq',
+            'MG.assembly_1_unmapped.R2.fq',
+            'MG.assembly_1_unmapped.SE.fq'], dir=A_OUT)
+    output:
+        '{dir}/MG.assembly_2.fa'.format(dir=A_OUT),
+    shell:
+        """
+        TMPD=$(mktemp -d -t --tmpdir={TMPDIR} "XXXXXX")
+        fq2fa --merge {input[0]} {input[1]} $TMPD/merged.fa
+        idba_ud -r $TMPD/merged.fa \
+        -l {input[2]} -o $TMPD \
+        --mink {config[idba_ud][mink]} --maxk {config[idba_ud][maxk]} \
+        --step {config[idba_ud][step]} --num_threads {THREADS} \
+        --similar {config[idba_ud][perid]} --pre_correction
+        mv $TMPD/contig.fa {output}
+        rm -rf $TMPD
+        """
+
+rule ASSEMBLY_MG_MERGE_ASSEMBLY:
+    log:
+        A_LOG
+    benchmark:
+        "%s/benchmarks/ASSEMBLY_MG_MERGE_ASSEMBLY.json" % A_OUT
+    input:
+        '{dir}/MG.assembly_1.fa'.format(dir=A_OUT),
+        '{dir}/MG.assembly_2.fa'.format(dir=A_OUT)
+    output:
+        '{dir}/final_assembly.fa'.format(dir=A_OUT),
+    shell:
+        """
+        NAME={A_OUT}/MG.assembly
+        cat {input} > $NAME.cat.fa
+        cap3 $NAME.cat.fa
+        # Concatenate assembled contigs, singletons and rename the contigs
+        cat $NAME.cat.fa.cap.contigs $NAME.cat.fa.cap.singlets | \
+        awk '/^>/{{print \">contig_\" ++i; next}}{{print}}' > $NAME.merged.fa
+        ln -s $NAME.merged.fa {output} && touch -h {output}
+        """