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HiS-NET-Seq_pipeline/Snakefile
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import os | |
sampleID = config["sampleID"] | |
WORKDIR = os.getcwd() | |
spikeIn = config["spikeIn"] | |
reference = config["reference"] | |
mask_bed = config["mask_bed"] | |
def resultFiles(spikeIn, reference, sampleID): | |
if spikeIn=="no" : | |
bigwigs=expand("BigWig/{sampleID}/{type}{sampleID}.{strand}.bw", sampleID=sampleID, type=["","PCRtrack_","RTtrack_"],strand = ["pos","neg"]) | |
if mask_bed!='': | |
masked=expand("Results/Masked_{sampleID}.{strand}.bedGraph", sampleID=sampleID, strand = ["pos","neg"]) | |
return bigwigs+masked | |
return bigwigs | |
else : | |
bedgraphs=expand("Bedgraphs/{sampleID}/{ref}/{type}{sampleID}.{strand}.bedGraph", sampleID=sampleID, ref = [reference,spikeIn], type=["","PCRtrack_","RTtrack_"],strand = ["pos","neg"]) | |
normalized=expand("Results/Normalized_{sampleID}.{strand}.bedGraph", sampleID=sampleID, strand = ["pos","neg"]) | |
if mask_bed!='': | |
masked=expand("Results/Masked_{sampleID}.{strand}.bedGraph", sampleID=sampleID, strand = ["pos","neg"]) | |
return bedgraphs+normalized+masked | |
return bedgraphs+normalized | |
rule all: | |
input: | |
resultFiles(spikeIn, reference, sampleID), | |
"Stats/"+sampleID+".csv" | |
rule create_link_fastq: | |
params: | |
file = config["file"], | |
out = WORKDIR+"/Data/" + sampleID + ".fastq." + config["compression"] | |
output: | |
temp("Data/" + sampleID + ".fastq." + config["compression"]) | |
threads: 1 | |
resources: | |
memory = 10, | |
time = 1 | |
shell: | |
"ln -s {params.file} {params.out}" | |
rule decompress: | |
input: | |
"Data/" + sampleID + ".fastq." + config["compression"] | |
output: | |
temp("TemporaryData/"+sampleID+".fastq") | |
params: | |
compression = config["compression"] | |
resources: | |
memory = 50, | |
time = 1 | |
threads: 1 | |
run: | |
if params.compression=="bz2": | |
shell("bunzip2 -c -k {input} > {output}") | |
elif params.compression=="gz": | |
shell("gunzip -c -k {input} > {output}") | |
elif params.compression=="no": | |
shell("cp {input} {output}") | |
rule remove_adapter: | |
input: | |
"TemporaryData/"+sampleID+".fastq" | |
output: | |
temp("TemporaryData/"+sampleID+"_noAdapter.fastq") | |
params: | |
cutadapt=config["cutadapt"], | |
cutadapt_params=config["cutadapt_params"], | |
min_len=config["barcode_len"] + 10 | |
resources: | |
memory = 100, | |
time = 4 | |
threads: | |
30 | |
shell: | |
"{params.cutadapt} {params.cutadapt_params} -m {params.min_len} -j {threads} -o {output} {input}" | |
rule fastqc: | |
input: | |
"TemporaryData/"+sampleID+"_noAdapter.fastq" | |
output: | |
"QC/"+sampleID+"_noAdapter_fastqc.html" | |
threads: | |
1 | |
params: | |
fastqc=config["fastqc"], | |
outdir=WORKDIR+"/QC/" | |
shell: | |
"{params.fastqc} --outdir={params.outdir} -i {input}" | |
rule collapse_reads: | |
input: | |
"TemporaryData/"+sampleID+"_noAdapter.fastq" | |
output: | |
"TemporaryData/"+sampleID+"_collapsed.txt" | |
params: | |
starcode=config["starcode"], | |
starcode_params=config["starcode_params"] | |
resources: | |
memory = 800, | |
time = 8 | |
threads: | |
10 | |
shell: | |
"{params.starcode} {params.starcode_params} -t {threads} -o {output} -i {input}" | |
rule barcode_dictionary: | |
input: | |
"TemporaryData/"+sampleID+"_collapsed.txt" | |
output: | |
"TemporaryData/"+sampleID+"_barcodes.pickle", | |
temp("TemporaryData/"+sampleID+"_noBC.fasta") | |
resources: | |
memory = 400, | |
time = 4 | |
threads: | |
1 | |
params: | |
barcode_len=config["barcode_len"] | |
script: | |
"source/createBarcodeDictionary.py" | |
rule map_reads: | |
input: | |
reads="TemporaryData/"+sampleID+"_noBC.fasta" | |
output: | |
temp("TemporaryData/Mapping/"+sampleID+"_Aligned.out.bam") | |
params: | |
input="TemporaryData/"+sampleID+"_noBC.fasta", | |
star=config["star"], | |
params=config["star_params"], | |
star_index=config["star_index"], | |
output_prefix="TemporaryData/Mapping/"+sampleID+"_" | |
resources: | |
memory = 200, | |
time = 4 | |
threads: | |
50 | |
shell: | |
"{params.star} --outSAMtype BAM Unsorted --genomeDir {params.star_index} --readFilesIn {params.input} --parametersFiles {params.params} --runThreadN {threads} --outFileNamePrefix {params.output_prefix}" | |
rule sort_bam: | |
input: | |
"TemporaryData/Mapping/"+sampleID+"_Aligned.out.bam" | |
output: | |
"TemporaryData/Mapping/"+sampleID+"_Aligned.sorted.bam" | |
params: | |
samtools=config["samtools"], | |
resources: | |
memory = 200, | |
time = 4 | |
threads: | |
10 | |
shell: | |
"{params.samtools} sort -@ {threads} -o {output} {input}" | |
rule parse_positions: | |
input: | |
"TemporaryData/"+sampleID+"_barcodes.pickle", | |
"TemporaryData/Mapping/"+sampleID+"_Aligned.sorted.bam" | |
output: | |
"TemporaryData/"+sampleID+"_posDict.pickle" | |
params: | |
barcode_len=config["barcode_len"], | |
resources: | |
memory = 300, | |
time = 4 | |
threads: | |
1 | |
script: | |
"source/parsePositions.py" | |
rule create_bedgraphs: | |
input: | |
"TemporaryData/"+sampleID+"_posDict.pickle", | |
output: | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_allReads.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_allReads.neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR.neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR_noSI.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR_noSI.neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+"PCRtrack_"+sampleID+".pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+"PCRtrack_"+sampleID+".neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+"RTtrack_"+sampleID+".pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+"RTtrack_"+sampleID+".neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+".pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+".neg.bedGraph" | |
params: | |
annotation=config["annotation"], | |
genome=config["genome_fa"], | |
barcode_len=config["barcode_len"], | |
barcode_linker=config["barcode_linker"], | |
threshold=0.05 | |
resources: | |
memory = 300, | |
time = 4 | |
threads: | |
1 | |
script: | |
"source/createBedgraphs.py" | |
rule create_stats: | |
input: | |
"TemporaryData/"+sampleID+".fastq", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_allReads.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_allReads.neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR.neg.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR_noSI.pos.bedGraph", | |
"Bedgraphs/"+sampleID+"/"+sampleID+"_noPCR_noSI.neg.bedGraph" | |
output: | |
"Stats/"+sampleID+".csv", | |
"Stats/Number_"+sampleID+".pdf", | |
"Stats/Percent_"+sampleID+".pdf" | |
params: | |
config["stats_bed"], | |
config["prefix"], | |
config["mask_downstream"] | |
resources: | |
memory = 100, | |
time = 10, | |
temp_memory = 100 | |
threads: | |
1 | |
script: | |
"source/createStats.py" | |
rule create_bw: | |
input: | |
bg = "Bedgraphs/"+sampleID+"/{X}.bedGraph" | |
output: | |
bw = "BigWig/"+sampleID+"/{X}.bw" | |
resources: | |
memory = 100, | |
time = 1 | |
params: | |
bedGraphToBigWig = config["bedGraphToBigWig"], | |
chrLen = config["star_index"] + "chrNameLength.txt" | |
threads: | |
1 | |
shell: | |
""" | |
sort -k1,1 -k2,2n {input.bg} > {input.bg}.temp | |
{params.bedGraphToBigWig} {input.bg}.temp {params.chrLen} {output.bw} | |
rm -f {input.bg}.temp | |
""" | |
rule splitBedgraph: | |
params: | |
prefix = config["prefix"], | |
input: | |
bg = "Bedgraphs/"+sampleID+"/{X}.bedGraph" | |
output: | |
reference_bg = "Bedgraphs/"+sampleID+"/"+reference+"/{X}.bedGraph", | |
spikeIn_bg = "Bedgraphs/"+sampleID+"/"+spikeIn+"/{X}.bedGraph" | |
resources: | |
memory = 10, | |
time = 1 | |
shell: | |
""" | |
grep -v {params.prefix} {input.bg} > {output.reference_bg} | |
grep {params.prefix} {input.bg} | sed "s/^{params.prefix}//g" > {output.spikeIn_bg} | |
""" | |
rule normalize_with_spikeIn: | |
input: | |
local_spike=expand("Bedgraphs/"+sampleID+"/"+spikeIn+"/"+sampleID+".{strand}.bedGraph", strand = ["pos","neg"]), | |
local_sample="Bedgraphs/"+sampleID+"/"+reference+"/{X}.bedGraph" | |
output: | |
"Results/Normalized_{X}.bedGraph", | |
"Results/factor_{X}.txt" | |
resources: | |
memory = 100, | |
time = 1 | |
threads: | |
1 | |
script: | |
"source/normalizeSpikeIn.py" | |
rule maskRegions: | |
input: | |
"Bedgraphs/"+sampleID+"/"+reference+"/{X}.bedGraph" | |
output: | |
"Results/Masked_{X}.bedGraph" | |
resources: | |
memory = 100, | |
time = 1 | |
threads: | |
1 | |
params: | |
config["mask_bed"] if config["mask_bed"]!="" else "" | |
script: | |
"source/maskRegion.py" |