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IGR-lab
ChIP-seq
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994fb238
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994fb238
authored
4 years ago
by
Laura Cook
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994fb238
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@@ -48,48 +48,66 @@ all_samples = IPS + unique_inputs
rule all:
input:
# expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/bwa/{sample}_{stage}_{mark}_q30.dupmark.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.dedup.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.dedup.bai", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}.dedup.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}.dupmark.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}.q30.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}.unfiltered.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
# "results/qc/multibamsum.npz",
# "results/qc/multibamsum.tab",
# "results/qc/pearsoncor_multibamsum.png",
# "results/qc/pearsoncor_multibamsum_matrix.txt",
# expand("results/qc/{sample}_{stage}_{mark}.SeqDepthNorm.bw", zip, sample=all_samples, stage=STAGE, mark=MARK),
# "results/qc/multiBAM_fingerprint.png",
# "results/qc/multiBAM_fingerprint_metrics.txt",
# "results/qc/multiBAM_fingerprint_rawcounts.txt",
# "results/qc/plot_coverage.png",
# "results/qc/plot_coverage_rawcounts.tab",
# expand("results/qc/{sample}_{stage}_{mark}.pbc.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}_filt_15Mreads.SE.cc.qc",zip, sample=all_samples, stage=STAGE, mark=MARK),
# expand("results/qc/{sample}_{stage}_{mark}_filt_15Mreads.SE.cc.plot.pdf", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/bwa/{sample}_{stage}_{mark}_q30.dupmark.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.dedup.bam", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/bwa/{sample}_{stage}_{mark}_q30.sorted.dedup.bai", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}.dedup.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}.dupmark.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}.q30.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}.unfiltered.flagstat.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
"results/bwa/E10.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/E11.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/E12.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/E13.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/E14.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/E15.5_H3K27ac_q30.sorted.pooled.dedup.bam",
"results/bwa/input_E10.5_H3K27ac_q30.sorted.dedup.bam",
"results/bwa/input_E11.5_H3K27ac_q30.sorted.dedup.bam",
"results/bwa/input_E12.5_H3K27ac_q30.sorted.dedup.bam",
"results/bwa/input_E13.5_H3K27ac_q30.sorted.dedup.bam",
"results/bwa/input_E14.5_H3K27ac_q30.sorted.dedup.bam",
"results/bwa/input_E15.5_H3K27ac_q30.sorted.dedup.bam",
"logs/E10.5_H3K27ac.mergeBAM",
"logs/E11.5_H3K27ac.mergeBAM",
"logs/E12.5_H3K27ac.mergeBAM",
"logs/E13.5_H3K27ac.mergeBAM",
"logs/E14.5_H3K27ac.mergeBAM",
"logs/E15.5_H3K27ac.mergeBAM",
"logs/input_E10.5_H3K27ac.mergeBAM",
"logs/input_E11.5_H3K27ac.mergeBAM",
"logs/input_E12.5_H3K27ac.mergeBAM",
"logs/input_E13.5_H3K27ac.mergeBAM",
"logs/input_E14.5_H3K27ac.mergeBAM",
"logs/input_E15.5_H3K27ac.mergeBAM",
"results/qc/multibamsum.npz",
"results/qc/multibamsum.tab",
"results/qc/pearsoncor_multibamsum.png",
"results/qc/pearsoncor_multibamsum_matrix.txt",
expand("results/qc/{sample}_{stage}_{mark}.SeqDepthNorm.bw", zip, sample=all_samples, stage=STAGE, mark=MARK),
"results/qc/multiBAM_fingerprint.png",
"results/qc/multiBAM_fingerprint_metrics.txt",
"results/qc/multiBAM_fingerprint_rawcounts.txt",
"results/qc/plot_coverage.png",
"results/qc/plot_coverage_rawcounts.tab",
expand("results/qc/{sample}_{stage}_{mark}.pbc.qc", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}_filt_15Mreads.SE.cc.qc",zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/qc/{sample}_{stage}_{mark}_filt_15Mreads.SE.cc.plot.pdf", zip, sample=all_samples, stage=STAGE, mark=MARK),
expand("results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_peaks.narrowPeak", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
expand("results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_peaks.xls", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
expand("results/macs2/{case}_vs_{control}_{stage}_{mark}_macs2_summits.bed", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
expand("logs/{case}_vs_{control}_{stage}_{mark}_call_peaks_macs2.log", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
# expand("results/macs2/{case}-vs-{control}_{stage}_{mark}-narrowpeak-count_mqc.json", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
# expand("results/bwa/{case}_{stage}_{mark}.bed", zip, case=IPS, stage=STAGE, mark=MARK),
# expand("logs/{case}_{stage}_{mark}.bamToBed", zip, case=IPS, stage=STAGE, mark=MARK),
# expand("results/frip/{case}_vs_{control}_{stage}_{mark}.frip.txt", case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
# expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
# expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
# expand("results/macs2/{stage}_{mark}_overlap.narrowPeak", zip, stage= STAGE, mark = MARK)
expand("results/bwa/{case}_{stage}_{mark}_q30.sorted.dedup.bed", zip, case=IPS, stage=STAGE, mark=MARK),
expand("logs/{case}_{stage}_{mark}.bamToBed", zip, case=IPS, stage=STAGE, mark=MARK),
expand("results/qc/{case}_vs_{control}_{stage}_{mark}.frip.txt", zip, case=IPS, control=INPUTS, stage=STAGE, mark=MARK),
directory("results/macs2/pooled"),
# "results/macs2/H3K27ac_E10.5_overlap.narrowPeak",
# "results/macs2/H3K27ac_E11.5_overlap.narrowPeak",
# "results/macs2/H3K27ac_E12.5_overlap.narrowPeak",
# "results/macs2/H3K27ac_E13.5_overlap.narrowPeak",
# "results/macs2/H3K27ac_E14.5_overlap.narrowPeak",
# "results/macs2/H3K27ac_E15.5_overlap.narrowPeak"
# expand("results/macs2/{stage}_H3K27ac_overlap.narrowPeak", zip, stage= STAGE, mark = MARK)
# directory("results/multiqc/multiqc_report_data/"),
# "results/multiqc/multiqc_report.html"
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