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updates to paired end files
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@jnhutchinson
jnhutchinson committed Dec 10, 2014
1 parent 344e07a commit 64c0c93
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Showing 5 changed files with 39 additions and 35 deletions.
23 changes: 14 additions & 9 deletions pipelines/RRBS_methylkit/compile_paired_results.sh
View file
@@ -1,6 +1,6 @@
fullfilename=$1
filename=$(basename $fullfilename)
sampleID=${filename%"_R1.trimmed.fq_bismark.coordsorted.methylkit.md"}
sampleID=${filename%"_R1_val_1.fq_bismark_pe.coordsorted.methylkit.md"}
sampleID1="${sampleID}_R1"
sampleID2="${sampleID}_R2"
QCreport="${sampleID}_QC_report.md"
Expand All @@ -18,23 +18,28 @@ echo -e "###${sampleID1}\n" >>$QCreport
sed 's/$/ /g' ${sampleID1}.fastq_trimming_report.txt >${sampleID1}.trimming.report.tmp
cat ${sampleID1}.trimming.report.tmp >>$QCreport
echo -e "\n[FASTQC before trimming](./fastqc/pretrim/${sampleID1}_fastqc/fastqc_report.html)\n" >>$QCreport
echo -e "\n[FASTQC after trimming](./fastqc/posttrim/${sampleID1}.val_1.fq_fastqc/fastqc_report.html)\n" >>$QCreport
echo -e "\n[FASTQC after trimming](./fastqc/posttrim/${sampleID1}_val_1.fq_fastqc/fastqc_report.html)\n" >>$QCreport
#sample2
echo -e "###${sampleID2}\n" >>$QCreport
sed 's/$/ /g' ${sampleID2}.fastq_trimming_report.txt >${sampleID2}.trimming.report.tmp
cat ${sampleID2}.trimming.report.tmp >>$QCreport
echo -e "\n[FASTQC before trimming](./fastqc/pretrim/${sampleID2}_fastqc/fastqc_report.html)\n" >>$QCreport
echo -e "\n[FASTQC after trimming](./fastqc/posttrim/${sampleID2}.val_2.fq_fastqc/fastqc_report.html)\n" >>$QCreport
echo -e "\n[FASTQC after trimming](./fastqc/posttrim/${sampleID2}_val_2.fq_fastqc/fastqc_report.html)\n" >>$QCreport

# mapping report
echo -e "\n##Bismark Alignment Report \n" >>$QCreport
sed 's/$/ /g' ${sampleID1}.val_1.fq_Bismark_paired-end_mapping_report.txt >${sampleID1}.mapping.report.tmp
cat ${sampleID}.mapping.report.tmp >>$QCreport
echo -e "\n##Bismark Alignment Report \n" >>$QCreport
if [ -f ${sampleID1}_val_1.fq_Bismark_paired-end_mapping_report.txt ]
then
sed 's/$/ /g' ${sampleID1}_val_1.fq_Bismark_paired-end_mapping_report.txt >${sampleID1}.mapping.report.tmp
cat ${sampleID1}.mapping.report.tmp >>$QCreport
rm ${sampleID1}.mapping.report.tmp
else
echo "${sampleID1}_val_1.fq_Bismark_paired-end_mapping_report.txt not found"
fi

# cleanup
rm ${sampleID}.mapping.report.tmp
rm ${sampleID}.trimming.report.tmp
rm ${sampleID}.trimming.report.tmp
rm ${sampleID1}.trimming.report.tmp
rm ${sampleID2}.trimming.report.tmp

#convert to html
pandoc -f markdown-yaml_metadata_block -t html -c http://dl.dropboxusercontent.com/u/4253254/CSS/GitHub2.css $QCreport -o ${sampleID}_QC_report.html
4 changes: 2 additions & 2 deletions pipelines/RRBS_methylkit/knitr_paired_quant_meth_methylkit.r
View file
Expand Up @@ -4,7 +4,7 @@ library(knitr)
args=commandArgs()
print(args)
samfilename=args[6] # coordinate sorted sam file from bismark alignment, passed at bpipe command line, specified in bpipe variables
sampleID=sub(".val_1.fq_bismark_pe.coordsorted.sam", "", basename(samfilename))
sampleID=sub(".fq_bismark_pe.coordsorted.sam", "", basename(samfilename))
dataDir=args[7] # directory with the sam file, passed at bpipe command line, specified in bpipe variables
methquantDir=paste(dataDir, "methylation_quantitation_results", sep="/")
build=args[8] # genomic build, passed at bpipe command line, specified in bpipe variables
Expand All @@ -14,7 +14,7 @@ minimumquality=args[11]

script_to_knit=file.path(scriptDir, "quant_meth_methylkit.rmd")
markdown_output=file.path(dataDir, "quant_meth_methylkit.md")
knit(input=script_to_knit, output=paste(sampleID, ".trimmed.fq_bismark.coordsorted.methylkit.md", sep=""), envir=environment())
knit(input=script_to_knit, output=paste(sampleID, ".fq_bismark_pe.coordsorted.methylkit.md", sep=""), envir=environment())


q()
4 changes: 2 additions & 2 deletions pipelines/RRBS_methylkit/knitr_quant_meth_methylkit.r
View file
Expand Up @@ -4,7 +4,7 @@ library(knitr)
args=commandArgs()
print(args)
samfilename=args[6] # coordinate sorted sam file from bismark alignment, passed at bpipe command line, specified in bpipe variables
sampleID=sub(".trimmed.fq_bismark.coordsorted.sam", "", basename(samfilename))
sampleID=sub("_val_1.trimmed.fq_bismark.coordsorted.sam", "", basename(samfilename))
dataDir=args[7] # directory with the sam file, passed at bpipe command line, specified in bpipe variables
methquantDir=paste(dataDir, "methylation_quantitation_results", sep="/")
build=args[8] # genomic build, passed at bpipe command line, specified in bpipe variables
Expand All @@ -14,7 +14,7 @@ minimumquality=args[11]

script_to_knit=file.path(scriptDir, "quant_meth_methylkit.rmd")
markdown_output=file.path(dataDir, "quant_meth_methylkit.md")
knit(input=script_to_knit, output=paste(sampleID, ".trimmed.fq_bismark.coordsorted.methylkit.md", sep=""), envir=environment())
knit(input=script_to_knit, output=paste(sampleID, "_val_1.trimmed.fq_bismark.coordsorted.methylkit.md", sep=""), envir=environment())


q()
41 changes: 20 additions & 21 deletions pipelines/RRBS_methylkit/rrbs_paired_trim_align_quant.groovy
View file
Expand Up @@ -34,34 +34,33 @@ mkfastqcdirs = {

//run fastqc on untrimmed
fastqc_pretrim = {
doc "Run FASTQC to generate QC metrics for the untrimmed reads"
output.dir = "${BASEDIR}/fastqc/pretrim/"
transform('.fastq') to('_fastqc.zip') {
doc "Run FASTQC to generate QC metrics for the untrimmed reads"
output.dir = "${BASEDIR}/fastqc/pretrim/"
transform('.fastq') to('_fastqc.zip') {
multi "fastqc -o $output.dir $input1.fastq",
"fastqc -o $output.dir $input2.fastq"
}
}
forward input
}

// Trim & fastqc
trim_galore = {
doc "Trim adapters and low quality bases from all reads"
output.dir = "${BASEDIR}"
from("fastq") {
transform('.fastq') to ('.val_*.fq'){
exec """
trim_galore ${RRBSVAR} ${DIRECTIONVAR}
--paired
--retain_unpaired
--fastqc
--fastqc_args "--outdir ${BASEDIR}/fastqc/posttrim"
--adapter ${ADAPTER}
--a2 ${ADAPTER}
--r1 ${MINTRIMMEDLENGTH}
--r2 ${MINTRIMMEDLENGTH}
--quality ${QUALITY} $input1.fastq $input2.fastq
"""
}
transform ('.fastq') to ('_val_*.fq'){
exec """
trim_galore ${RRBSVAR} ${DIRECTIONVAR}
--paired
--retain_unpaired
--fastqc
--fastqc_args "--outdir ${BASEDIR}/fastqc/posttrim"
--adapter ${ADAPTER}
--a2 ${ADAPTER}
--length ${MINTRIMMEDLENGTH}
--r1 ${MINTRIMMEDLENGTH}
--r2 ${MINTRIMMEDLENGTH}
--quality ${QUALITY} $input1.fastq $input2.fastq
"""
}
}

Expand All @@ -87,7 +86,7 @@ sortsam = {
//quantitate methylation with methylkit, sam files will be parsed and CpG C/T conversions counted for each individual sample
quantmeth = {
doc "Quantitate methylation with methylKit"
transform('.val_1.fq_bismark_pe.coordsorted.sam') to ('.trimmed.fq_bismark.coordsorted.methylkit.md') {
transform('.fq_bismark_pe.coordsorted.sam') to ('.fq_bismark_pe.coordsorted.methylkit.md') {
exec """
${SCRIPTDIR}/knitr_paired_quant_meth_methylkit.r $input $BASEDIR $BUILD $SCRIPTDIR $MINIMUMCOVERAGE $MINIMUMQUALITY
""", "quantmeth"
Expand Down
2 changes: 1 addition & 1 deletion pipelines/RRBS_methylkit/rrbs_trim_align_quant.groovy
View file
Expand Up @@ -49,7 +49,7 @@ trim_galore = {
doc "Trim adapters and low quality bases from all reads"
output.dir = "${BASEDIR}"
from("fastq") {
transform('.fastq') to ('.trimmed.fq'){
produce ('fq'){
exec """
trim_galore ${RRBSVAR} ${DIRECTIONVAR}
--fastqc
Expand Down

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