From 994fb2381a130b540bfd3c6aa7d1bafa955b1397 Mon Sep 17 00:00:00 2001
From: Laura Cook <l.cook2@student.unimelb.edu.au>
Date: Fri, 28 Aug 2020 14:41:51 +1000
Subject: [PATCH] fixed rule all
---
mouse/Snakefile | 94 +++++++++++++++++++++++++++++--------------------
1 file changed, 56 insertions(+), 38 deletions(-)
diff --git a/mouse/Snakefile b/mouse/Snakefile
index bbb72d0..bd9ffae 100644
--- a/mouse/Snakefile
+++ b/mouse/Snakefile
@@ -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"
--
GitLab