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    "info": {
        "author": "bars",
        "author_email": "barslmn@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Topic :: Software Development :: Build Tools"
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        "description": "# Pigeon\n\n## Introduction\nTool for pipeing inputs and outputs of multiple cli tools.\nPigeon takes in only a config file as input. Everything required to run the pipeline are specified in config file. The config file is specified according to [python configparser](https://docs.python.org/3.4/library/configparser.html).\n\n## Quick Install\n#### Linux&Mac  \n\n> sudo pip3 install --index-url https://test.pypi.org/simple/ pigeon\n\n#### Windows  \n\n> pip install --index-url https://test.pypi.org/simple/ pigeon\n\n## Resources for NGS\nNone of the tools or data files are supplemented by pigeon so they need to be downloaded.\nFor example configuration file, exome sequencing pipeline,\n\n* Tools\n    + [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n    + [BWA](https://github.com/lh3/bwa)\n    + [Picard](https://broadinstitute.github.io/picard/)\n    + [GATK](https://software.broadinstitute.org/gatk/)\n    + [Annotation Tool](https://test.pypi.org/project/dove/)\n* Reference Files\n    + [Reference genome and known SNP&INDELS](https://software.broadinstitute.org/gatk/download/bundle)\n        * hg19 or\n        * hg38\n    + Bed file\n        * See website of capture kit used in sequencing\n\n## How to use\nCreate yourself a configuration file\n\n> pigeon createconfig\n\nModify for your analysis. (See below.)\n\n> pigeon -c my_config.conf -d\n\nIf everything looks alright run for real.\n\n> pigeon -c my_config.conf\n\n## Config File\n\nConfig file consists of three parts.\n\n* General\n* Pipeline\n* Individual tool blocks\n\n## General\nArea used to define project name, output directory, input files, and resource files like reference genome or target file. Following variables are necessary for run.\n\nRequired:\n\n* project_name : name of your project\n* output_dir : where to write output files\n* input_files : input files for analysis, space separated, pairs should be next to each other. e.g.\n\n  > input_files = A.txt B.txt C.txt  \n\n  or for paired \n\n  > input_files = A1.txt A2.txt B1.txt B2.txt C1.txt C2.txt\n\nOptional variable can also be decleared here. Based on your or tool requirements. Later these variables can be called in the config file using ${GENERAL:optional_variable}.\n\nOptional(example): \n\n> reference_genome = /path/to/my/reference_genome.fa\n\n> bed_file = /path/to/my/target.bed\n\n> known_snp = /path/to/my/snp.vcf\n\n> my_database = /path/to/my/favorite.db\n\n## Pipeline\nThis area should contain paths to tools that is understanble by your shell. As well as the run order of tools. e.g.\n\n> pipeline = job1 job2 job3\n\n> A = path/to/A\n\n> B = path/to/B\n\n> C = path/to/C\n\n## Tool Blocks\nName of the block should be same as in **pipeline**. By continuing example above;\n\n> [job1]\n\n> [job2]\n\n> [job3]\n\nArguments that can be used in these blocks as follows:\n\n#### Run Args\n\n* tool: tool variable from pipeline block. e.g.\n\n  > tool = ${PIPELINE:A}\n\n* sub_tool: if tool has a sub tool like 'bwa mem'. e.g.\n\n  > sub_tool = mem\n\n* args: arguments of the tools\n* java: if tool is a jar file add java -jar before it.\n* pass: if True it won't run the block. But the block still be part of the pipeline. This option is helpful for resuming interrupted pipeline.\n\n#### Input Args\n* input_from: Name of the block that that's output is this jobs input. First jobs input_from should be input_files.\n* input_multi: can be 'paired' or 'all'. Paired option splits input files stream into groups of two. All option uses all of the input files.\n* input_flag_repeat: If tool requires input flag for each input this command will add given flag before each input.\n\n* secondary_in_placeholder\n\n#### Output Args\n\n* suffix: add suffix to output file name\n* ext: file extension of the output\n* dump_dir: creates a directory and outputs there.\n\n* paired_output: this option will pair the input and the output of the tool.\n\n* secondary_out_placeholder\n* secondary_suffix\n* secondary_ext\n* secondary_dump_dir\n\n#### Placeholders\nThese are joker words that can be used in **args**. \n\n* input_placeholder\n* secondary_input_placeholder\n\n* output_placeholder\n* secondary_output_placeholder\n\n### Example Config\n\n> [[GENERAL]]  \n> project_name = my_project  \n> output_dir = /path/to/output_directory  \n> input_files = A.txt B.txt C.txt  \n> my_db = /path/to/my.db  \n\n> [[PIPELINE]]  \n> pipeline = job1 job2 job3  \n> A = /path/to/A  \n> B = /path/to/B  \n> C = /path/to/C  \n\n> [job1]  \n> tool = A  \n> input_from = input_files  \n> args = -i input_placeholder -o output_placeholder  \n> suffix = job1_A  \n> ext = txt  \n\n> [job2]  \n> tool = B  \n> input_from = job1  \n> args = -i input_placeholder -o output_placeholder  \n> suffix = job2_B  \n> ext = txt  \n\n> [job3]  \n> tool = C  \n> input_from = job2  \n> args = -i input_placeholder -o output_placeholder  \n> suffix = job3_C  \n> ext = txt  \n\n\n\n",
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