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fixed ppqt
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@tovahmarkowitz
tovahmarkowitz committed Nov 29, 2018
2 parents 3ab0d0e + 4c6c5fb commit 4a33bd7
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Showing 2 changed files with 79 additions and 182 deletions.
84 changes: 33 additions & 51 deletions Rules/InitialChIPseqQC.snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -277,30 +277,6 @@ samtools index {output.outbam2}
samtools flagstat {output.outbam2} > {output.flagstat2}
"""

rule ppqt_se:
input:
bam1= join(workpath,bam_dir,"{name}.sorted.bam"),
bam4= join(workpath,bam_dir,"{name}.sorted.Q5DD.bam"),
output:
ppqt1= join(workpath,bam_dir,"{name}.sorted.ppqt"),
pdf1= join(workpath,bam_dir,"{name}.sorted.pdf"),
ppqt4= join(workpath,bam_dir,"{name}.sorted.Q5DD.ppqt"),
pdf4= join(workpath,bam_dir,"{name}.sorted.Q5DD.pdf"),
params:
rname="pl:ppqt",
batch='--mem=24g --time=10:00:00 --gres=lscratch:800',
samtoolsver=config['bin'][pfamily]['tool_versions']['SAMTOOLSVER'],
rver=config['bin'][pfamily]['tool_versions']['RVER'],
shell: """
module load {params.samtoolsver};
module load {params.rver};
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c={input.bam1} -savp -out={output.ppqt1} -tmpdir=/lscratch/$SLURM_JOBID -rf
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c={input.bam4} -savp -out={output.ppqt4} -tmpdir=/lscratch/$SLURM_JOBID -rf
"""


if pe == 'yes':
rule InitialChIPseqQC:
params:
Expand Down Expand Up @@ -447,33 +423,39 @@ samtools index {output.outbam2}
samtools flagstat {output.outbam2} > {output.flagstat2}
"""

rule ppqt_pe:
input:
bam1= join(workpath,bam_dir,"{name}.sorted.bam"),
bam4= join(workpath,bam_dir,"{name}.sorted.Q5DD.bam"),
output:
ppqt1= join(workpath,bam_dir,"{name}.sorted.ppqt"),
pdf1= join(workpath,bam_dir,"{name}.sorted.pdf"),
ppqt4= join(workpath,bam_dir,"{name}.sorted.Q5DD.ppqt"),
pdf4= join(workpath,bam_dir,"{name}.sorted.Q5DD.pdf"),
params:
rname="pl:ppqt",
batch='--mem=24g --time=10:00:00 --gres=lscratch:800',
samtoolsver=config['bin'][pfamily]['tool_versions']['SAMTOOLSVER'],
rver=config['bin'][pfamily]['tool_versions']['RVER'],
shell:
"""
module load {params.samtoolsver};
module load {params.rver};
samtools view -b -f 66 -o /lscratch/$SLURM_JOBID/bam1.f66.bam {input.bam1}
samtools index /lscratch/$SLURM_JOBID/bam1.f66.bam
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c=/lscratch/$SLURM_JOBID/bam1.f66.bam -savp={output.pdf1} -out={output.ppqt1} -tmpdir=/lscratch/$SLURM_JOBID -rf
samtools view -b -f 66 -o /lscratch/$SLURM_JOBID/bam4.f66.bam {input.bam4}
samtools index /lscratch/$SLURM_JOBID/bam4.f66.bam
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c=/lscratch/$SLURM_JOBID/bam4.f66.bam -savp={output.pdf4} -out={output.ppqt4} -tmpdir=/lscratch/$SLURM_JOBID -rf
"""
rule ppqt:
input:
bam1= join(workpath,bam_dir,"{name}.sorted.bam"),
bam4= join(workpath,bam_dir,"{name}.sorted.Q5DD.bam"),
output:
ppqt1= join(workpath,bam_dir,"{name}.sorted.ppqt"),
pdf1= join(workpath,bam_dir,"{name}.sorted.pdf"),
ppqt4= join(workpath,bam_dir,"{name}.sorted.Q5DD.ppqt"),
pdf4= join(workpath,bam_dir,"{name}.sorted.Q5DD.pdf"),
params:
rname="pl:ppqt",
batch='--mem=24g --time=10:00:00 --gres=lscratch:800',
samtoolsver=config['bin'][pfamily]['tool_versions']['SAMTOOLSVER'],
rver=config['bin'][pfamily]['tool_versions']['RVER'],
run:
commoncmd="module load {params.samtoolsver};module load {params.rver};"
if se=="yes":
cmd1="Rscript Scripts/phantompeakqualtools/run_spp.R \
-c={input.bam1} -savp -out={output.ppqt1} -tmpdir=/lscratch/$SLURM_JOBID -rf;"
cmd4="Rscript Scripts/phantompeakqualtools/run_spp.R \
-c={input.bam4} -savp -out={output.ppqt4} -tmpdir=/lscratch/$SLURM_JOBID -rf"
elif pe=="yes":
cmd1="samtools view -b -f 66 -o /lscratch/$SLURM_JOBID/bam1.f66.bam {input.bam1}; \
samtools index /lscratch/$SLURM_JOBID/bam1.f66.bam; \
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c=/lscratch/$SLURM_JOBID/bam1.f66.bam -savp={output.pdf1} -out={output.ppqt1} \
-tmpdir=/lscratch/$SLURM_JOBID -rf;"
cmd4="samtools view -b -f 66 -o /lscratch/$SLURM_JOBID/bam4.f66.bam {input.bam4}; \
samtools index /lscratch/$SLURM_JOBID/bam4.f66.bam; \
Rscript Scripts/phantompeakqualtools/run_spp.R \
-c=/lscratch/$SLURM_JOBID/bam4.f66.bam -savp={output.pdf4} -out={output.ppqt4} \
-tmpdir=/lscratch/$SLURM_JOBID -rf"
shell(commoncmd+cmd1+cmd4)

rule picard_dedup:
input:
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