04 December 2014

XML+XSLT = #Makefile -based #workflows for #bioinformatics

I've recently read some conversations on Twitter about Makefile-based bioinformatics workflows. I've suggested on biostars.org (Standard simple format to describe a bioinformatics analysis pipeline) that a XML file could be used to describe a model of data and XSLT could transform this model to a Makefile-based workflow. I've already explored this idea in a previous post (Generating a pipeline of analysis (Makefile) for NGS with xslt. ) and in our lab, we use JSON and jsvelocity to generate our workflows (e.g: https://gist.github.com/lindenb/3c07ca722f793cc5dd60).
In the current post, I'll describe my github repository containing a complete XML+XSLT example: https://github.com/lindenb/ngsxml.

Download the data

git clone "https://github.com/lindenb/ngsxml.git"


The model
The XML model is self-explanatory:
<?xml version="1.0" encoding="UTF-8"?>
<model name="myProject" description="my project" directory="OUT">
  <project name="Proj1">
    <sample name="Sample1">
      <fastq>
        <for>test/fastq/sample_1_01_R1.fastq.gz</for>
        <rev>test/fastq/sample_1_01_R2.fastq.gz</rev>
      </fastq>
      <fastq id="groupid2" lane="2" library="lib1" platform="ILMN" median-size="98">
        <for>test/fastq/sample_1_02_R1.fastq.gz</for>
        <rev>test/fastq/sample_1_02_R2.fastq.gz</rev>
      </fastq>
    </sample>
    <sample name="Sample2">
      <fastq>
        <for>test/fastq/sample_2_01_R1.fastq.gz</for>
        <rev>test/fastq/sample_2_01_R2.fastq.gz</rev>
      </fastq>
    </sample>
  </project>
</model>


Validating the model:
This XML document is possibly validated with a XML schema: 
$ xmllint  --schema xsd/schema01.xsd --noout test/model01.xml
test/model01.xml validates


Generating the Makefile:
The XML document is transformed into a Makefile using the following XSLT stylesheet: https://github.com/lindenb/ngsxml/blob/master/stylesheets/model2make.xsl
xsltproc --output Makefile stylesheets/model2make.xsl test/model01.xml
The Makefile:
# Name
#  myProject
# Description:
#  my project
# 
include config.mk
OUTDIR=OUT
BINDIR=$(abspath ${OUTDIR})/bin


# if tools are undefined
bwa.exe ?=${BINDIR}/bwa-0.7.10/bwa
samtools.exe ?=${BINDIR}/samtools-0.1.19/samtools
bcftools.exe ?=${BINDIR}/samtools-0.1.19/bcftools/bcftools
tabix.exe ?=${BINDIR}/tabix-0.2.6/tabix
bgzip.exe ?=${BINDIR}/tabix-0.2.6/bgzip

.PHONY=all clean all_bams all_vcfs

all: all_vcfs


all_vcfs:  \
 $(OUTDIR)/Projects/Proj1/VCF/Proj1.vcf.gz


all_bams:  \
 $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam \
 $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam

#
# VCF for project 'Proj1'
# 
$(OUTDIR)/Projects/Proj1/VCF/Proj1.vcf.gz : $(addsuffix .bai, $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam) \
 $(addsuffix .fai,${REFERENCE}) ${samtools.exe}  ${bgzip.exe} ${tabix.exe} ${bcftools.exe}
 mkdir -p $(dir $@) && \
 ${samtools.exe} mpileup -uf ${REFERENCE} $(basename $(filter %.bai,$^)) | \
 ${bcftools.exe} view -vcg - > $(basename $@)  && \
 ${bgzip.exe} -f $(basename $@) && \
 ${tabix.exe} -f -p vcf $@
 
    



#
# index final BAM for Sample 'Sample1'
# 
$(addsuffix .bai, $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam): $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${samtools.exe} index  $<
#
# prepare final BAM for Sample 'Sample1'
# 
$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam : $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}rmdup.bam
 mkdir -p $(dir $@) && \
 cp  $< $@


$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}rmdup.bam : $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}merged.bam ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${samtools.exe} rmdup  $<  $@



#
# merge BAMs 
#
$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}merged.bam :  \
  $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}1_sorted.bam \
  $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}2_sorted.bam ${samtools.exe}
 mkdir -p $(dir $@) && \
  ${samtools.exe} merge -f $@ $(filter %.bam,$^)
  



 
#
# Index BAM $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}1_sorted.bam
#
$(addsuffix .bai,$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}1_sorted.bam ): $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}1_sorted.bam ${samtools.exe}
 ${samtools} index $<

#
# Align test/fastq/sample_1_01_R1.fastq.gz and test/fastq/sample_1_01_R2.fastq.gz
#
$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}1_sorted.bam : \
 test/fastq/sample_1_01_R1.fastq.gz  \
 test/fastq/sample_1_01_R2.fastq.gz \
 $(addsuffix .bwt,${REFERENCE}) \
 ${bwa.exe} ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${bwa.exe} mem -R '@RG\tID:idp20678948\tSM:Sample1\tLB:Sample1\tPL:ILLUMINA\tPU:1' \
  ${REFERENCE} \
  test/fastq/sample_1_01_R1.fastq.gz \
  test/fastq/sample_1_01_R2.fastq.gz |\
 ${samtools.exe} view -uS - |\
 ${samtools.exe} sort - $(basename $@) 





 
#
# Index BAM $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}2_sorted.bam
#
$(addsuffix .bai,$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}2_sorted.bam ): $(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}2_sorted.bam ${samtools.exe}
 ${samtools} index $<

#
# Align test/fastq/sample_1_02_R1.fastq.gz and test/fastq/sample_1_02_R2.fastq.gz
#
$(OUTDIR)/Projects/Proj1/Samples/Sample1/BAM/${tmp.prefix}2_sorted.bam : \
 test/fastq/sample_1_02_R1.fastq.gz  \
 test/fastq/sample_1_02_R2.fastq.gz \
 $(addsuffix .bwt,${REFERENCE}) \
 ${bwa.exe} ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${bwa.exe} mem -R '@RG\tID:groupid2\tSM:Sample1\tLB:lib1\tPL:ILMN\tPU:2\tPI:98' \
  ${REFERENCE} \
  test/fastq/sample_1_02_R1.fastq.gz \
  test/fastq/sample_1_02_R2.fastq.gz |\
 ${samtools.exe} view -uS - |\
 ${samtools.exe} sort - $(basename $@) 




#
# index final BAM for Sample 'Sample2'
# 
$(addsuffix .bai, $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam): $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${samtools.exe} index  $<
#
# prepare final BAM for Sample 'Sample2'
# 
$(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam : $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}rmdup.bam
 mkdir -p $(dir $@) && \
 cp  $< $@


$(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}rmdup.bam : $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}1_sorted.bam ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${samtools.exe} rmdup  $<  $@





 
#
# Index BAM $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}1_sorted.bam
#
$(addsuffix .bai,$(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}1_sorted.bam ): $(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}1_sorted.bam ${samtools.exe}
 ${samtools} index $<

#
# Align test/fastq/sample_2_01_R1.fastq.gz and test/fastq/sample_2_01_R2.fastq.gz
#
$(OUTDIR)/Projects/Proj1/Samples/Sample2/BAM/${tmp.prefix}1_sorted.bam : \
 test/fastq/sample_2_01_R1.fastq.gz  \
 test/fastq/sample_2_01_R2.fastq.gz \
 $(addsuffix .bwt,${REFERENCE}) \
 ${bwa.exe} ${samtools.exe}
 mkdir -p $(dir $@) && \
 ${bwa.exe} mem -R '@RG\tID:idp20681172\tSM:Sample2\tLB:Sample2\tPL:ILLUMINA\tPU:1' \
  ${REFERENCE} \
  test/fastq/sample_2_01_R1.fastq.gz \
  test/fastq/sample_2_01_R2.fastq.gz |\
 ${samtools.exe} view -uS - |\
 ${samtools.exe} sort - $(basename $@) 




$(addsuffix .fai,${REFERENCE}): ${REFERENCE} ${samtools.exe}
 ${samtools.exe} faidx $<

$(addsuffix .bwt,${REFERENCE}): ${REFERENCE} ${bwa.exe}
 ${bwa.exe} index $<


${BINDIR}/bwa-0.7.10/bwa :
 rm -rf $(BINDIR)/bwa-0.7.10/ && \
 mkdir -p $(BINDIR) && \
 curl -o $(BINDIR)/bwa-0.7.10.tar.bz2 -L "http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.10.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj $(BINDIR)/bwa-0.7.10.tar.bz2 -C $(OUTDIR)/bin  && \
 rm $(BINDIR)/bwa-0.7.10.tar.bz2 && \
 make -C $(dir $@)

${BINDIR}/samtools-0.1.19/bcftools/bcftools: ${BINDIR}/samtools-0.1.19/samtools

${BINDIR}/samtools-0.1.19/samtools  : 
 rm -rf $(BINDIR)/samtools-0.1.19/ && \
 mkdir -p $(BINDIR) && \
 curl -o $(BINDIR)/samtools-0.1.19.tar.bz2 -L "http://sourceforge.net/projects/samtools/files/samtools-0.1.19.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj $(BINDIR)/samtools-0.1.19.tar.bz2 -C $(OUTDIR)/bin  && \
 rm $(BINDIR)/samtools-0.1.19.tar.bz2 && \
 make -C $(dir $@)


${BINDIR}/tabix-0.2.6/bgzip : ${BINDIR}/tabix-0.2.6/tabix


${BINDIR}/tabix-0.2.6/tabix  : 
 rm -rf $(BINDIR)/tabix-0.2.6/ && \
 mkdir -p $(BINDIR) && \
 curl -o $(BINDIR)/tabix-0.2.6.tar.bz2 -L "http://sourceforge.net/projects/samtools/files/tabix-0.2.6.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj $(BINDIR)/tabix-0.2.6.tar.bz2 -C $(OUTDIR)/bin  && \
 rm $(BINDIR)/tabix-0.2.6.tar.bz2 && \
 make -C $(dir $@) tabix bgzip

clean:
 rm -rf ${BINDIR}
Drawing the Workflow:
The workflow is drawn with https://github.com/lindenb/makefile2graph.


Running Make:
And here is the output of make:
rm -rf /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/ && \
 mkdir -p /home/lindenb/src/ngsxml/OUT/bin && \
 curl -o /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10.tar.bz2 -L "http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.10.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10.tar.bz2 -C OUT/bin  && \
 rm /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10.tar.bz2 && \
 make -C /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/
bwa-0.7.10/
bwa-0.7.10/bamlite.c
(...)
gcc -g -Wall -Wno-unused-function -O2 -msse -msse2 -msse3 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
make[1]: Entering directory `/home/lindenb/src/ngsxml'
/home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/bwa index test/ref/ref.fa
rm -rf /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/ && \
 mkdir -p /home/lindenb/src/ngsxml/OUT/bin && \
 curl -o /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19.tar.bz2 -L "http://sourceforge.net/projects/samtools/files/samtools-0.1.19.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19.tar.bz2 -C OUT/bin  && \
 rm /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19.tar.bz2 && \
 make -C /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/
samtools-0.1.19/
samtools-0.1.19/.gitignore
samtools-0.1.19/AUTHORS
(...)
gcc -g -Wall -O2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
make[3]: Leaving directory `/home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/misc'
make[2]: Leaving directory `/home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19'
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/bwa mem -R '@RG\tID:idp11671724\tSM:Sample1\tLB:Sample1\tPL:ILLUMINA\tPU:1' \
  test/ref/ref.fa \
  test/fastq/sample_1_01_R1.fastq.gz \
  test/fastq/sample_1_01_R2.fastq.gz |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools view -uS - |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools sort - OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__1_sorted 
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/bwa mem -R '@RG\tID:groupid2\tSM:Sample1\tLB:lib1\tPL:ILMN\tPU:2\tPI:98' \
  test/ref/ref.fa \
  test/fastq/sample_1_02_R1.fastq.gz \
  test/fastq/sample_1_02_R2.fastq.gz |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools view -uS - |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools sort - OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__2_sorted 
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
  /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools merge -f OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__merged.bam OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__1_sorted.bam OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__2_sorted.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools rmdup  OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__merged.bam  OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__rmdup.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
 cp  OUT/Projects/Proj1/Samples/Sample1/BAM/__DELETE__rmdup.bam OUT/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample1/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools index  OUT/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample2/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/bwa-0.7.10/bwa mem -R '@RG\tID:idp11673828\tSM:Sample2\tLB:Sample2\tPL:ILLUMINA\tPU:1' \
  test/ref/ref.fa \
  test/fastq/sample_2_01_R1.fastq.gz \
  test/fastq/sample_2_01_R2.fastq.gz |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools view -uS - |\
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools sort - OUT/Projects/Proj1/Samples/Sample2/BAM/__DELETE__1_sorted 
mkdir -p OUT/Projects/Proj1/Samples/Sample2/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools rmdup  OUT/Projects/Proj1/Samples/Sample2/BAM/__DELETE__1_sorted.bam  OUT/Projects/Proj1/Samples/Sample2/BAM/__DELETE__rmdup.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample2/BAM/ && \
 cp  OUT/Projects/Proj1/Samples/Sample2/BAM/__DELETE__rmdup.bam OUT/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam
mkdir -p OUT/Projects/Proj1/Samples/Sample2/BAM/ && \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools index  OUT/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam
/home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools faidx test/ref/ref.fa
rm -rf /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6/ && \
 mkdir -p /home/lindenb/src/ngsxml/OUT/bin && \
 curl -o /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6.tar.bz2 -L "http://sourceforge.net/projects/samtools/files/tabix-0.2.6.tar.bz2/download?use_mirror=freefr" && \
 tar xvfj /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6.tar.bz2 -C OUT/bin  && \
 rm /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6.tar.bz2 && \
 make -C /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6/ tabix bgzip
tabix-0.2.6/
tabix-0.2.6/ChangeLog
tabix-0.2.6/Makefile
(...)
make[2]: Leaving directory `/home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6'
mkdir -p OUT/Projects/Proj1/VCF/ && \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/samtools mpileup -uf test/ref/ref.fa OUT/Projects/Proj1/Samples/Sample1/BAM/Proj1_Sample1.bam OUT/Projects/Proj1/Samples/Sample2/BAM/Proj1_Sample2.bam | \
 /home/lindenb/src/ngsxml/OUT/bin/samtools-0.1.19/bcftools/bcftools view -vcg - > OUT/Projects/Proj1/VCF/Proj1.vcf  && \
 /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6/bgzip -f OUT/Projects/Proj1/VCF/Proj1.vcf && \
 /home/lindenb/src/ngsxml/OUT/bin/tabix-0.2.6/tabix -f -p vcf OUT/Projects/Proj1/VCF/Proj1.vcf.gz
make[1]: Leaving directory `/home/lindenb/src/ngsxml'
At the end, a VCF is generated
##fileformat=VCFv4.1
##samtoolsVersion=0.1.19-44428cd
(...)
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1 Sample2
chr4_gl000194_random 1973 . C G 14.4 . DP=3;VDB=2.063840e-02;AF1=1;AC1=4;DP4=0,0,3,0;MQ=60;FQ=-32.3 GT:PL:GQ 1/1:31,6,0:11 1/1:17,3,0:8
chr4_gl000194_random 2462 . A T 14.4 . DP=3;VDB=2.063840e-02;AF1=1;AC1=4;DP4=0,0,0,3;MQ=60;FQ=-32.3 GT:PL:GQ 1/1:31,6,0:11 1/1:17,3,0:8
chr4_gl000194_random 2492 . G C 14.4 . DP=3;VDB=2.063840e-02;AF1=1;AC1=4;DP4=0,0,0,3;MQ=60;FQ=-32.3 GT:PL:GQ 1/1:31,6,0:11 1/1:17,3,0:8
chr4_gl000194_random 2504 . A T 14.4 . DP=3;VDB=2.063840e-02;AF1=1;AC1=4;DP4=0,0,0,3;MQ=60;FQ=-32.3 GT:PL:GQ 1/1:31,6,0:11 1/1:17,3,0:8
That's it,

Pierre

Publié par Pierre Lindenbaum at 8:40 PM

Libellés : , , , , , ,

1 comment:

Marmaduke said...

Wow. That's pretty slick. Thanks for sharing!

Friday, 12 December, 2014

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