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| project_name: "test_ChIP-seq" | ||
| project_dir: "~/projects/test_ChIP-seq" | ||
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| ## Aligner: bowtie or bowtie2 | ||
| aligner: "bowtie" | ||
| pair_end: "yes" | ||
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| ## If use bowtie, then bowtie1 index path to be assigned here. | ||
| ## "Genome" replaced by genome name as "hg19" or "mm9", and | ||
| ## uncomment next line. | ||
| bowtie_index: "~/data/bowtie_index/Genome" | ||
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| ## If use bowtie2, then "Genome" should be replace by | ||
| ## bowtie2 index name, as "hg19" or "mm9" | ||
| ## $BOWTIE2_INDEXES should be added in the environment variables | ||
| # bowtie_index: "Genome" | ||
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| bam_sort_buff: "2G" | ||
| IGV_genome: "hg19" | ||
| # ngsplot_genome: "reference_genome" | ||
| # ngsplot_fraglen: 150 | ||
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| ## the folder under project folder, containing fastq folder. | ||
| data_dir: "data" | ||
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| ## match pattern for input files. Now it could be: | ||
| ## *.fastq, *.fq, *.gz | ||
| ## for pair end data, use "*R1*.fastq.gz" or "*R1*.fastq" | ||
| input_files: "*R1*.fastq.gz" | ||
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| ## cluster settings | ||
| cores: 4 # number of cores to use for multi-threaded programs. | ||
| queue: "queue_name" | ||
| h_vmem: "32G" | ||
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| ## wall_time for every step, hh:mm | ||
| wall_time: | ||
| alignFastqByBowtie: "23:59" | ||
| runFastqc: "4:00" | ||
| rmdupBam: "20:00" | ||
| genTDF: "20:00" | ||
| runPhantomPeak: "20:00" |
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| #! /usr/bin/env python | ||
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| import os | ||
| import sys | ||
| import yaml | ||
| from ruffus import * | ||
| import glob | ||
| import subprocess | ||
| import string | ||
| import drmaa | ||
| from ruffus.drmaa_wrapper import run_job, error_drmaa_job | ||
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| my_drmaa_session = drmaa.Session() | ||
| my_drmaa_session.initialize() | ||
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| def expandOsPath(path): | ||
| """ | ||
| To expand the path with shell variables. | ||
| Arguments: | ||
| - `path`: path string | ||
| """ | ||
| return os.path.expanduser(os.path.expandvars(path)) | ||
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| def genFilesWithPattern(pathList, Pattern): | ||
| """ | ||
| To generate files list on the fly based on wildcards pattern. | ||
| Arguments: | ||
| - `pathList`: the path of the files | ||
| - `Pattern`: pattern like config["input_files"] | ||
| """ | ||
| pathList.append(Pattern) | ||
| Files = expandOsPath(os.path.join(*pathList)) | ||
| return Files | ||
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| def cluster_options(config, task_name, cores, logfile): | ||
| """ | ||
| Generate a string of cluster options to feed an LSF job. | ||
| Arguments: | ||
| - `config`: configuration as associative array from the YAML file. | ||
| - `task_name`: the specific task name, such as runPhantomPeak. | ||
| - `cores`: number of cores to use for this task. | ||
| - `logfile`: log file name. | ||
| """ | ||
| ## Here are the paramters for SGE. | ||
| str_options = "-cwd -V -pe shm %d -q %s -j y -o %s" % \ | ||
| (cores, config["queue"], logfile) | ||
| if "h_vmem" in config: | ||
| str_options = str_options + " -l h_vmem=%s" % (config["h_vmem"]) | ||
| return str_options | ||
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| config_name = sys.argv[1] | ||
| config_f = open(config_name, "r") | ||
| config = yaml.load(config_f) | ||
| config_f.close() | ||
| inputfiles = expandOsPath(os.path.join(config["project_dir"], config["data_dir"], "fastq", config["input_files"])) | ||
| FqFiles = [x for x in glob.glob(inputfiles)] | ||
| fq_name, fq_ext = os.path.splitext(config["input_files"]) | ||
| fq_ext_suffix = ".alignment.log" | ||
| Bam_path = expandOsPath(os.path.join(config["project_dir"], config["data_dir"])) + "/" | ||
| FastQC_path = expandOsPath(os.path.join(config["project_dir"], config["data_dir"], "FastQC")) | ||
| rmdup_path = expandOsPath(os.path.join(config["project_dir"], config["data_dir"], "rmdup")) | ||
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| scipt_path = os.path.dirname(os.path.realpath(__file__)) | ||
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| @transform(FqFiles, formatter(fq_ext), os.path.join(Bam_path, "{basename[0]}.bam"), config) | ||
| def alignFastqByBowtie(FqFileName, OutputBamFileName, config): | ||
| """ | ||
| To align '.fastq' to genome. | ||
| Arguments: | ||
| - `FqFileName`: file to be processed | ||
| """ | ||
| if "aligner" in config: | ||
| if config["aligner"] == "bowtie": | ||
| cmds = ['fastq2bam_by_bowtie.sh'] | ||
| cmds.append(FqFileName) | ||
| cmds.append(expandOsPath(config['bowtie_index'])) | ||
| elif config["aligner"] == "bowtie2": | ||
| cmds = ['fastq2bam_by_bowtie2.sh'] | ||
| cmds.append(FqFileName) | ||
| cmds.append(config['bowtie_index']) | ||
| else: | ||
| raise KeyError | ||
| else: | ||
| cmds = ['fastq2bam_by_bowtie.sh'] | ||
| cmds.append(FqFileName) | ||
| cmds.append(expandOsPath(config['bowtie_index'])) | ||
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| target = expandOsPath(os.path.join(config["project_dir"], config["data_dir"])) | ||
| cmds.append(target) | ||
| cmds.append(config["pair_end"]) | ||
| cores = int(config['cores']) | ||
| if cores == 0: | ||
| cores = 1 | ||
| cmds.append(str(cores)) | ||
| logfile = FqFileName + ".alignment.log" | ||
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| run_job(" ".join(cmds), | ||
| job_name = "alignFastqByBowtie_" + os.path.basename(FqFileName), | ||
| job_other_options = cluster_options(config, "alignFastqByBowtie", cores, logfile), | ||
| job_script_directory = os.path.dirname(os.path.realpath(__file__)), | ||
| job_environment={ 'BASH_ENV' : '/srv/gsfs0/home/nshao/.bashrc' }, | ||
| retain_job_scripts = True, drmaa_session=my_drmaa_session) | ||
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| return 0 | ||
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| @follows(alignFastqByBowtie, mkdir(FastQC_path)) | ||
| @transform(alignFastqByBowtie, suffix(".bam"), ".bam.fastqc.log", config) | ||
| def runFastqc(BamFileName, fastqcLog, config): | ||
| """ | ||
| To run FastQC | ||
| Arguments: | ||
| - `BamFileName`: bam file | ||
| - `config`: config | ||
| """ | ||
| cmds = ['fastqc'] | ||
| cmds.append("-o") | ||
| cmds.append(expandOsPath(os.path.join(config["project_dir"], config["data_dir"], "FastQC"))) | ||
| cores = int(config['cores']) | ||
| if cores == 0: | ||
| cores = 1 | ||
| cmds.append("-t") | ||
| cmds.append(str(cores)) | ||
| cmds.append(BamFileName) | ||
| logfile = BamFileName + ".fastqc.log" | ||
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| run_job(" ".join(cmds), | ||
| job_name = "fastqc_" + os.path.basename(BamFileName), | ||
| job_other_options = cluster_options(config, "runFastqc", cores, logfile), | ||
| job_script_directory = os.path.dirname(os.path.realpath(__file__)), | ||
| job_environment={ 'BASH_ENV' : '~/.bashrc' }, | ||
| retain_job_scripts = True, drmaa_session=my_drmaa_session) | ||
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| return 0 | ||
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| @follows(runFastqc, mkdir(rmdup_path)) | ||
| @transform(alignFastqByBowtie, formatter(".bam"), os.path.join(rmdup_path, "{basename[0]}_rmdup.bam"), config) | ||
| def rmdupBam(BamFileName, rmdupFile, config): | ||
| """ | ||
| To remove duplicates | ||
| Arguments: | ||
| - `BamFileName`: bam file | ||
| - `config`: config | ||
| """ | ||
| if config["pair_end"]=="no": | ||
| cmds = ['rmdup.bam.sh'] | ||
| else: | ||
| cmds = ['rmdup_PE.bam.sh'] | ||
| cmds.append(BamFileName) | ||
| cmds.append(rmdup_path) | ||
| #if "bam_sort_buff" in config: | ||
| # cmds.append(config["bam_sort_buff"]) | ||
| logfile = BamFileName + ".rmdup.log" | ||
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| cores = 1 | ||
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| run_job(" ".join(cmds), | ||
| job_name = "rmdup_" + os.path.basename(BamFileName), | ||
| job_other_options = cluster_options(config, "rmdupBam", cores, logfile), | ||
| job_script_directory = os.path.dirname(os.path.realpath(__file__)), | ||
| job_environment={ 'BASH_ENV' : '~/.bashrc' }, | ||
| retain_job_scripts = True, drmaa_session=my_drmaa_session) | ||
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| return 0 | ||
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| @follows(rmdupBam, mkdir(expandOsPath(os.path.join(rmdup_path, "tdf")))) | ||
| @transform(rmdupBam, suffix(".bam"), ".bam.tdf.log", config) | ||
| def genTDF(BamFileName, tdfLog, config): | ||
| """ | ||
| To generate TDF files for IGV | ||
| Arguments: | ||
| - `BamFileName`: bam file | ||
| - `config`: config | ||
| """ | ||
| cmds = ['igvtools'] | ||
| cmds.append("count") | ||
| cmds.append(BamFileName) | ||
| TDFPath = expandOsPath(os.path.join(rmdup_path, "tdf")) | ||
| baseName = os.path.basename(BamFileName) | ||
| cmds.append(os.path.join(TDFPath, baseName.replace(".bam", ".tdf"))) | ||
| cmds.append(config["IGV_genome"]) | ||
| logfile = BamFileName + ".tdf.log" | ||
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| cores = 1 | ||
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| run_job(" ".join(cmds), | ||
| job_name = "genTDF_" + os.path.basename(BamFileName), | ||
| job_other_options = cluster_options(config, "genTDF", cores, logfile), | ||
| job_script_directory = os.path.dirname(os.path.realpath(__file__)), | ||
| job_environment={ 'BASH_ENV' : '~/.bashrc' }, | ||
| retain_job_scripts = True, drmaa_session=my_drmaa_session) | ||
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| return 0 | ||
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| @follows(genTDF) | ||
| @transform(rmdupBam, suffix(".bam"), ".bam.phantomPeak.log", config) | ||
| def runPhantomPeak(BamFileName, Log, config): | ||
| """ | ||
| To check data with phantomPeak | ||
| Arguments: | ||
| - `BamFileName`: bam file | ||
| - `config`: config | ||
| """ | ||
| cmds = ['runPhantomPeak.sh'] | ||
| cmds.append(BamFileName) | ||
| cmds.append(str(config["cores"])) | ||
| logfile = BamFileName + ".phantomPeak.log" | ||
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| cores = int(config['cores']) | ||
| if cores == 0: | ||
| cores = 1 | ||
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| run_job(" ".join(cmds), | ||
| job_name = "runPhantomPeak_" + os.path.basename(BamFileName), | ||
| job_other_options = cluster_options(config, "runPhantomPeak", cores, logfile), | ||
| job_script_directory = os.path.dirname(os.path.realpath(__file__)), | ||
| job_environment={ 'BASH_ENV' : '~/.bashrc' }, | ||
| retain_job_scripts = True, drmaa_session=my_drmaa_session) | ||
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| return 0 | ||
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| if __name__ == '__main__': | ||
| ## run to step of PhantomPeak | ||
| ## multithread number need to be changed! | ||
| pipeline_run([runPhantomPeak], multithread=200) | ||
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| my_drmaa_session.exit() |
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