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Verified Commit 81909f3f authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
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for test data, disable macs2 model

parent 17e92926
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Showing with 21 additions and 21 deletions
workflow/rules/common.smk
View file @ 81909f3f
......@@ -246,11 +246,11 @@ def get_multiqc_input(wildcards):
"results/picard_dedup/{sample}.picard_dedup.stats.txt",
"results/bamtools_filtered/{sample}.sorted.bamtools_filtered.flagstat",
"results/bamtools_filtered/{sample}.sorted.bamtools_filtered.idxstats",
"results/bamtools_filtered/{sample}.sorted.bamtools_filtered.stats.txt",
"results/phantompeakqualtools/{sample}.phantompeak.spp.out",
"results/phantompeakqualtools/{sample}.spp_correlation_mqc.tsv",
"results/phantompeakqualtools/{sample}.spp_nsc_mqc.tsv",
"results/phantompeakqualtools/{sample}.spp_rsc_mqc.tsv"
"results/bamtools_filtered/{sample}.sorted.bamtools_filtered.stats.txt"
#"results/phantompeakqualtools/{sample}.phantompeak.spp.out",
#"results/phantompeakqualtools/{sample}.spp_correlation_mqc.tsv",
#"results/phantompeakqualtools/{sample}.spp_nsc_mqc.tsv",
#"results/phantompeakqualtools/{sample}.spp_rsc_mqc.tsv"
],
sample = sample
)
......@@ -338,8 +338,8 @@ def all_input(wildcards):
if is_single_end(sample, unit):
wanted_input.extend(expand(
[
"results/trimmed_se/{sample}-{unit}.fastq.gz"#,
#"results/trimmed_se/{sample}-{unit}.settings"
"results/trimmed_se/{sample}-{unit}.fastq.gz",
"results/trimmed_se/{sample}-{unit}.settings"
],
sample = sample,
unit = unit
......@@ -349,8 +349,8 @@ def all_input(wildcards):
wanted_input.extend(
expand (
[
"results/trimmed_pe/{sample}-{unit}.R1.fastq.gz",
"results/trimmed_pe/{sample}-{unit}.R2.fastq.gz",
"results/trimmed_pe/{sample}-{unit}.1.fastq.gz",
"results/trimmed_pe/{sample}-{unit}.2.fastq.gz",
"results/trimmed_pe/{sample}-{unit}.settings"
],
sample = sample,
......@@ -360,14 +360,14 @@ def all_input(wildcards):
# mapping, merging and filtering bam-files
for sample in samples.index:
wanted_input.extend(
expand (
[
"results/phantompeakqualtools/{sample}.phantompeak.pdf"
],
sample = sample
)
)
#wanted_input.extend(
# expand (
# [
# "results/phantompeakqualtools/{sample}.phantompeak.pdf"
# ],
# sample = sample
# )
#)
if config["params"]["deeptools-plots"]["activate"]:
wanted_input.extend(
......
workflow/rules/peak_analysis.smk
View file @ 81909f3f
......@@ -57,8 +57,8 @@ rule macs2_callpeak_broad:
)
log:
"logs/macs2/callpeak.{sample}-{control}.broad.log"
params:
lambda w, input:"--broad-cutoff 0.1 -f {bam_format} {gsize} -B --SPMR --keep-dup all {pvalue} {qvalue}".format(
params: # --nomodel --extsize 147 added for fake data
lambda w, input:"--broad-cutoff 0.1 -f {bam_format} {gsize} --nomodel --extsize 147 -B --SPMR --keep-dup all {pvalue} {qvalue}".format(
gsize="{}".format(open(input.gsizepath).read().strip()),
pvalue="-p {}".format(config["params"]["callpeak"]["p-value"]) if config["params"]["callpeak"]["p-value"] else "",
qvalue="-q {}".format(config["params"]["callpeak"]["q-value"]) if config["params"]["callpeak"]["q-value"] else "",
......@@ -217,7 +217,7 @@ rule plot_macs_qc:
conda:
"../envs/plot_macs_annot.yaml"
shell:
"Rscript ../workflow/scripts/plot_macs_qc.R -i {params.input} -s {params.sample_control_combinations} "
"Rscript workflow/scripts/plot_macs_qc.R -i {params.input} -s {params.sample_control_combinations} "
"-o {output.plot} -p {output.summmary} 2> {log}"
rule plot_homer_annotatepeaks:
......@@ -237,7 +237,7 @@ rule plot_homer_annotatepeaks:
conda:
"../envs/plot_macs_annot.yaml"
shell:
"Rscript ../workflow/scripts/plot_homer_annotatepeaks.R -i {params.input} "
"Rscript workflow/scripts/plot_homer_annotatepeaks.R -i {params.input} "
"-s {params.sample_control_combinations} -o {output.plot} -p {output.summmary} 2> {log}"
rule plot_sum_annotatepeaks:
......
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