flow recipes

metagenomics.R

## a vector of full paths to fastq files (mate 1)
fqs1 = rep("myfile.fastq", 20)
## a vector of full paths to fastq files (mate 2)
fqs2 = rep("myfile.fastq", 20)
## full path to bwa
bwa_exe = ""
bwa_aln_opts = ""
bwa_sampe_opts = ""

## reference library
reflib = ""

## path to java: full path
java_exe = "java"
java_mem = "-Xmx8g"
## path to javatmp
java_tmp = "~/tmp"
## path to picard_dir
picard_dir = "tmp"

## path to samtools
samtools_exe = "samtools"



############### create commands, make into a function later on
sai_files1=file.path(gsub(".fastq.gz",".sai",basename(fqs1)))
sai_files2=file.path( gsub(".fastq.gz",".sai",basename(fqs2)))
bam_files=file.path(gsub(".fastq.gz",".bam",basename(fqs1)))
cmd_aln1 <- sprintf("%s aln %s %s %s > %s",bwa_exe, bwa_aln_opts,reflib,fqs1, sai_files1)
cmd_aln2 <- sprintf("%s aln %s %s %s > %s",bwa_exe, bwa_aln_opts,reflib,fqs2, sai_files2)
cmd_sampe <- sprintf("%s sampe %s %s %s %s %s %s | %s view -Shu - > %s",
                     bwa_exe,bwa_sampe_opts,reflib,sai_files1,sai_files2,fqs1,fqs2,samtools_exe, bam_files)
## ----------------- START read group
bamrg_files=sprintf("%s_rg.bam",bam_files)
cmd_fixrg <- sprintf("%s %s -Djava.io.tmpdir=%s -jar %s/AddOrReplaceReadGroups.jar INPUT=%s OUTPUT=%s SORT_ORDER=coordinate RGID=%s RGLB=%s RGPL=%s RGPU=%s RGSM=%s RGCN=%s VALIDATION_STRINGENCY=LENIENT",
                       java_exe, java_mem, java_tmp, picard_dir, bam_files, 
                       bamrg_files, rgid, rglb, platform, rgpu, rgsm,
                       center)
## ----------------- START merging
mergebam <- file.path(out_bampath,out_bam)
bam_list <- paste("INPUT=", bamrg_files, sep = "", collapse = " ")
java_mem <- "-Xmx8g";
cmd_merge <- sprintf("%s %s -Djava.io.tmpdir=%s -jar %s/MergeSamFiles.jar %s OUTPUT=%s ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true USE_THREADING=true",
                       java_exe, java_mem, java_tmp, picard_dir, bam_list, mergebam)
                       
cmd_list <- list(aln1 = cmd_aln1, aln2 = cmd_aln2, sampe = cmd_sampe)
                       

recipies.sh

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