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Commit b4fe9787 authored by Rachel LEGENDRE's avatar Rachel LEGENDRE
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change IA/IDR output name for IGV session

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...@@ -502,7 +502,7 @@ else: ...@@ -502,7 +502,7 @@ else:
# Coverage step # Coverage step
#---------------------------------- #----------------------------------
if config["bamCoverage"]["do"]: if config["bamCoverage"]["do"]:
bamCoverage_input = os.path.join(analysis_dir, "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)) bamCoverage_input = "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)
bamCoverage_logs = os.path.join(analysis_dir, "12-IGV/logs/{SAMPLE}_{REF}.out") bamCoverage_logs = os.path.join(analysis_dir, "12-IGV/logs/{SAMPLE}_{REF}.out")
bamCoverage_output = os.path.join(analysis_dir, "12-IGV/{SAMPLE}_{REF}_coverage.bw") bamCoverage_output = os.path.join(analysis_dir, "12-IGV/{SAMPLE}_{REF}_coverage.bw")
bamCoverage_options = config['bamCoverage']['options'] bamCoverage_options = config['bamCoverage']['options']
...@@ -513,7 +513,7 @@ if config["bamCoverage"]["do"]: ...@@ -513,7 +513,7 @@ if config["bamCoverage"]["do"]:
#---------------------------------- #----------------------------------
# Estimate Library Complexity # Estimate Library Complexity
#---------------------------------- #----------------------------------
lib_complexity_input = os.path.join(analysis_dir, "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)) lib_complexity_input = "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)
lib_complexity_metrics = os.path.join(analysis_dir, "05-QC/Complexity/{SAMPLE}_{REF}_metrics.txt") lib_complexity_metrics = os.path.join(analysis_dir, "05-QC/Complexity/{SAMPLE}_{REF}_metrics.txt")
lib_complexity_log_std = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.out") lib_complexity_log_std = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.out")
lib_complexity_log_err = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.err") lib_complexity_log_err = os.path.join(analysis_dir, "05-QC/Complexity/logs/{SAMPLE}_{REF}_complexity.err")
...@@ -524,7 +524,7 @@ include: os.path.join(RULES, "EstimateLibraryComplexity.rules") ...@@ -524,7 +524,7 @@ include: os.path.join(RULES, "EstimateLibraryComplexity.rules")
# plot Fingerprint # plot Fingerprint
#---------------------------------- #----------------------------------
def IPandINPUT(wildcards): def IPandINPUT(wildcards):
return [str(os.path.join(analysis_dir, biasedRegions_dir +"/") + IP_INPUT[IP_INPUT.IP == wildcards.IP].iloc[0]['INPUT'] + "_{}_sort_dedup{}.bam".format(ref, biasedRegions)), os.path.join(analysis_dir,"{}/{{IP}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions))] return [str(biasedRegions_dir + "/" + IP_INPUT[IP_INPUT.IP == wildcards.IP].iloc[0]['INPUT'] + "_{}_sort_dedup{}.bam".format(ref, biasedRegions)), "{}/{{IP}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)]
plotFingerprint_input = IPandINPUT plotFingerprint_input = IPandINPUT
...@@ -559,11 +559,11 @@ if config['geneBody']['do']: ...@@ -559,11 +559,11 @@ if config['geneBody']['do']:
# fragment size distribution - Picard CollectInsertSizeMetrics # fragment size distribution - Picard CollectInsertSizeMetrics
#------------------------------------------------ #------------------------------------------------
if paired: if paired:
insert_size_metrics_input = os.path.join(analysis_dir, "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)) insert_size_metrics_input = "{}/{{SAMPLE}}_{{REF}}_sort_dedup{}.bam".format(biasedRegions_dir, biasedRegions)
insert_size_metrics_output_txt = "05-QC/FragmentSizeDistribution/{SAMPLE}_{REF}_sort_dedup_fragmentSizeDistribution.txt" insert_size_metrics_output_txt = os.path.join(analysis_dir, "05-QC/FragmentSizeDistribution/{SAMPLE}_{REF}_sort_dedup_fragmentSizeDistribution.txt")
insert_size_metrics_histo = "05-QC/FragmentSizeDistribution/{SAMPLE}_{REF}_sort_dedup_fragmentSizeDistribution.pdf" insert_size_metrics_histo = os.path.join(analysis_dir, "05-QC/FragmentSizeDistribution/{SAMPLE}_{REF}_sort_dedup_fragmentSizeDistribution.pdf")
insert_size_metrics_log_out = "05-QC/FragmentSizeDistribution/logs/{SAMPLE}_{REF}_fragment_size.out" insert_size_metrics_log_out = os.path.join(analysis_dir, "05-QC/FragmentSizeDistribution/logs/{SAMPLE}_{REF}_fragment_size.out")
insert_size_metrics_log_err = "05-QC/FragmentSizeDistribution/logs/{SAMPLE}_{REF}_fragment_size.err" insert_size_metrics_log_err = os.path.join(analysis_dir, "05-QC/FragmentSizeDistribution/logs/{SAMPLE}_{REF}_fragment_size.err")
final_output.extend(expand(insert_size_metrics_output_txt, SAMPLE=samples, REF=ref)) final_output.extend(expand(insert_size_metrics_output_txt, SAMPLE=samples, REF=ref))
include: os.path.join(RULES, "fragment_size_distribution.rules") include: os.path.join(RULES, "fragment_size_distribution.rules")
...@@ -638,7 +638,7 @@ else : ...@@ -638,7 +638,7 @@ else :
#---------------------------------- #----------------------------------
if config["macs2"]["do"]: if config["macs2"]["do"]:
def INPUTtoIP(wildcards): def INPUTtoIP(wildcards):
return str(os.path.join(analysis_dir,biasedRegions_dir) + "/" + IP_INPUT[IP_INPUT.IP == wildcards.SAMPLE].iloc[0]['INPUT'] + "_{}_sort_dedup{}.bam".format(ref, biasedRegions)) return str(biasedRegions_dir + "/" + IP_INPUT[IP_INPUT.IP == wildcards.SAMPLE].iloc[0]['INPUT'] + "_{}_sort_dedup{}.bam".format(ref, biasedRegions))
model = config["macs2"]["mode_choice"] model = config["macs2"]["mode_choice"]
model_dir = model model_dir = model
...@@ -657,7 +657,6 @@ if config["macs2"]["do"]: ...@@ -657,7 +657,6 @@ if config["macs2"]["do"]:
config["macs2"]['cutoff']) + config["macs2"]['options'] config["macs2"]['cutoff']) + config["macs2"]['options']
if config["macs2"]["no_model"]: if config["macs2"]["no_model"]:
macs2_options += " --nomodel " macs2_options += " --nomodel "
#macs2_input_done += [os.path.join(analysis_dir, "05-PhantomPeakQualTools/{{IP}}_{}_sort_dedup{}_spp.out".format(ref, biasedRegions))]
macs2_shift_file = os.path.join(analysis_dir, "05-QC/PhantomPeakQualTools/{{SAMPLE}}_{}_sort_dedup{}_spp.out".format(ref, biasedRegions)) macs2_shift_file = os.path.join(analysis_dir, "05-QC/PhantomPeakQualTools/{{SAMPLE}}_{}_sort_dedup{}_spp.out".format(ref, biasedRegions))
else: else:
macs2_shift_file = "Empty" macs2_shift_file = "Empty"
...@@ -666,8 +665,7 @@ if config["macs2"]["do"]: ...@@ -666,8 +665,7 @@ if config["macs2"]["do"]:
else: else:
macs2_pe_mode = "no" macs2_pe_mode = "no"
macs2_input_bam = os.path.join(analysis_dir, "{}/{{SAMPLE}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)) macs2_input_bam = "{}/{{SAMPLE}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)
#macs2_control = "{}/{{INPUT}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)
macs2_control = INPUTtoIP macs2_control = INPUTtoIP
macs2_log = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/logs/{{SAMPLE}}.out".format(model_dir)) macs2_log = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/logs/{{SAMPLE}}.out".format(model_dir))
macs2_output = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/{{SAMPLE}}_peaks.{}Peak".format(model_dir, model)) macs2_output = os.path.join(analysis_dir, "06-PeakCalling/macs2/{}/{{SAMPLE}}_peaks.{}Peak".format(model_dir, model))
...@@ -696,7 +694,7 @@ if config["seacr"]["do"]: ...@@ -696,7 +694,7 @@ if config["seacr"]["do"]:
include: os.path.join(RULES, "compute_scaling_factor.rules") include: os.path.join(RULES, "compute_scaling_factor.rules")
# produce bedgrah files # produce bedgrah files
bedgraph_input = os.path.join(analysis_dir, "{}/{{SAMPLE}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)) bedgraph_input = "{}/{{SAMPLE}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)
if config["design"]["spike"]: if config["design"]["spike"]:
bedgraph_scaleFactor = compute_scaling_factor_output bedgraph_scaleFactor = compute_scaling_factor_output
else: else:
...@@ -793,7 +791,7 @@ if config["macs2"]["do"] and model in ["narrow"] and not config["intersectionApp ...@@ -793,7 +791,7 @@ if config["macs2"]["do"] and model in ["narrow"] and not config["intersectionApp
select_peaks_input_ppr = IDR_input_ppr select_peaks_input_ppr = IDR_input_ppr
select_peaks_input_pool = IDR_input_pool select_peaks_input_pool = IDR_input_pool
select_peaks_logs = os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}_{}/logs/{{IP_IDR}}_selected_peaks.o".format(model_dir)) select_peaks_logs = os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}_{}/logs/{{IP_IDR}}_selected_peaks.o".format(model_dir))
select_peaks_output = os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}_{}/{{IP_IDR}}_select.Peak".format(model_dir)) select_peaks_output = os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}_{}/{{IP_IDR}}_select.{}Peak".format(model_dir, model))
include: os.path.join(RULES, "select_peaks.rules") include: os.path.join(RULES, "select_peaks.rules")
final_output.extend(expand(select_peaks_output, CALLER="macs2", IP_IDR=IP_REP)) final_output.extend(expand(select_peaks_output, CALLER="macs2", IP_IDR=IP_REP))
...@@ -816,7 +814,7 @@ def IA_input(wildcards): ...@@ -816,7 +814,7 @@ def IA_input(wildcards):
if (config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"]) or config["intersectionApproach"]["do"] or config["seacr"]["do"] : if (config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"]) or config["intersectionApproach"]["do"] or config["seacr"]["do"] :
intersectionApproach_input_rep = IA_input intersectionApproach_input_rep = IA_input
intersectionApproach_logs = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/logs/{IP_IDR}_IA_peaks.o") intersectionApproach_logs = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/logs/{IP_IDR}_IA_peaks.o")
intersectionApproach_output = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{IP_IDR}_IA.Peak") intersectionApproach_output = os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{IP_IDR}_IA.bed")
if config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"] : if config["macs2"]["do"] and config["macs2"]["mode_choice"] in ["broad"] :
intersectionApproach_overlap = 0.8 intersectionApproach_overlap = 0.8
else: else:
...@@ -852,10 +850,10 @@ if len(conds) > 1 and config["differential_analysis"]["do"]: ...@@ -852,10 +850,10 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
def getPeakFilesByMark(wildcards): def getPeakFilesByMark(wildcards):
if wildcards.CALLER in ["seacr_"+config["seacr"]["threshold"], "macs2_broad" ] or (wildcards.CALLER in ["macs2_narrow"] and config["intersectionApproach"]["do"]): if wildcards.CALLER in ["seacr_"+config["seacr"]["threshold"], "macs2_broad" ] or (wildcards.CALLER in ["macs2_narrow"] and config["intersectionApproach"]["do"]):
return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{MARK}_{COND}_IA.Peak"), return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{MARK}_{COND}_IA.bed"),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds) CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
else : else :
return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{CALLER}/{MARK}_{COND}_select.Peak"), return expand(os.path.join(analysis_dir, "08-ReproduciblePeaks/{{CALLER}}/{{MARK}}_{{COND}}_select.{}Peak".format(model)),
CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds) CALLER=wildcards.CALLER, MARK=wildcards.MARK, COND=conds)
...@@ -907,7 +905,7 @@ if len(conds) > 1 and config["differential_analysis"]["do"]: ...@@ -907,7 +905,7 @@ if len(conds) > 1 and config["differential_analysis"]["do"]:
feature_counts_input = getBAMFilesByMark feature_counts_input = getBAMFilesByMark
feature_counts_optional_input = [] feature_counts_optional_input = []
if config["differential_analysis"]["input_counting"]: if config["differential_analysis"]["input_counting"]:
feature_counts_optional_input += expand(os.path.join(analysis_dir, "{}/{{INPUT}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions)), INPUT=CORR_INPUT) feature_counts_optional_input += expand("{}/{{INPUT}}_{}_sort_dedup{}.bam".format(biasedRegions_dir, ref, biasedRegions), INPUT=CORR_INPUT)
feature_counts_output_count = os.path.join(analysis_dir, "09-CountMatrix/{CALLER}/{MARK}_Matrix_Optimal_Peak.mtx") feature_counts_output_count = os.path.join(analysis_dir, "09-CountMatrix/{CALLER}/{MARK}_Matrix_Optimal_Peak.mtx")
if len(conds) == 2 : if len(conds) == 2 :
feature_counts_gff = os.path.join(analysis_dir, "09-CountMatrix/{{CALLER}}/{{MARK}}_{}u{}_{}.optimal.Peak_overlap.gff".format(conds[0], conds[1], ref)) feature_counts_gff = os.path.join(analysis_dir, "09-CountMatrix/{{CALLER}}/{{MARK}}_{}u{}_{}.optimal.Peak_overlap.gff".format(conds[0], conds[1], ref))
......
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