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        "description": "# [PyPPL][3] - A [Py](#)thon [P](#)i[P](#)e[L](#)ine framework\n\n[![Pypi][10]][18] [![Github][11]][3] [![PythonVers][14]][18] [![docs][19]][1] [![Travis building][5]][7] [![Codacy][4]][8] [![Codacy coverage][6]][8]\n\n[Documentation][1] | [API][2] | [Change log][9]\n\n<!-- toc -->\n## Features\n- Process caching.\n- Process reusability.\n- Process error handling.\n- Runner customization.\n- Easy running profile switching.\n- Plugin system.\n\n## Installation\n```bash\npip install PyPPL\n```\n\n## Plugin gallery\n\n(*) shipped with `PyPPL`\n\n- [pyppl_report](https://github.com/pwwang/pyppl_report): Generating reports for PyPPL pipelines\n- [pyppl_flowchart](https://github.com/pwwang/pyppl_flowchart): Generating flowchart for PyPPL\n- [pyppl_export](https://github.com/pwwang/pyppl_export)*: Exporting outputs generated by PyPPL pipeline\n- [pyppl_echo](https://github.com/pwwang/pyppl_echo)*: Echoing script output to PyPPL logs\"\n- [pyppl_rich](https://github.com/pwwang/pyppl_rich)*: Richer information in logs for PyPPL\n- [pyppl_strict](https://github.com/pwwang/pyppl_strict)*: More strict check of job success for PyPPL\n- [pyppl_lock](https://github.com/pwwang/pyppl_lock)*: Preventing running processes from running again for PyPPL\n- [pyppl_annotate](https://github.com/pwwang/pyppl_annotate): Adding long description/annotation for processes\n- [pyppl_require](https://github.com/pwwang/pyppl_require): Checking and installing requirements for processes\n- [pyppl_jobtime](https://github.com/pwwang/pyppl_jobtime): Job running time statistics for PyPPL\n- [pyppl_notify](https://github.com/pwwang/pyppl_notify): Email notifications for PyPPL\n- [pyppl_runcmd](https://github.com/pwwang/pyppl_runcmd): Allowing to run local command before and after each process for PyPPL\n- [pyppl_runners](https://github.com/pwwang/pyppl_runners): Common runners for PyPPL\n\n## Writing pipelines with predefined processes\nLet's say we are implementing the [TCGA DNA-Seq Re-alignment Workflow][16]\n(The very left part of following figure).\nFor demonstration, we will skip the QC and the co-clean parts here.\n\n[![DNA_Seq_Variant_Calling_Pipeline][15]][16]\n\n`demo.py`:\n```python\nfrom pyppl import PyPPL, Channel\n# import predefined processes\nfrom TCGAprocs import pBamToFastq, pAlignment, pBamSort, pBamMerge, pMarkDups\n\n# Load the bam files\npBamToFastq.input = Channel.fromPattern('/path/to/*.bam')\n# Align the reads to reference genome\npAlignment.depends = pBamToFastq\n# Sort bam files\npBamSort.depends = pAlignment\n# Merge bam files\npBamMerge.depends = pBamSort\n# Mark duplicates\npMarkDups.depends = pBamMerge\n# Export the results\npMarkDups.config.export_dir = '/path/to/realigned_Bams'\n# Specify the start process and run the pipeline\nPyPPL().start(pBamToFastq).run()\n```\n\n[![asciicast][20]][21]\n\n## Implementing individual processes\n`TCGAprocs.py`:\n```python\nfrom pyppl import Proc\npBamToFastq = Proc(desc = 'Convert bam files to fastq files.')\npBamToFastq.input = 'infile:file'\npBamToFastq.output = [\n    'fq1:file:{{i.infile | stem}}_1.fq.gz',\n    'fq2:file:{{i.infile | stem}}_2.fq.gz']\npBamToFastq.script = '''\nbamtofastq collate=1 exclude=QCFAIL,SECONDARY,SUPPLEMENTARY \\\n    filename= {{i.infile}} gz=1 inputformat=bam level=5 \\\n    outputdir= {{job.outdir}} outputperreadgroup=1 tryoq=1 \\\n    outputperreadgroupsuffixF=_1.fq.gz \\\n    outputperreadgroupsuffixF2=_2.fq.gz \\\n    outputperreadgroupsuffixO=_o1.fq.gz \\\n    outputperreadgroupsuffixO2=_o2.fq.gz \\\n    outputperreadgroupsuffixS=_s.fq.gz\n'''\n\npAlignment = Proc(desc = 'Align reads to reference genome.')\npAlignment.input = 'fq1:file, fq2:file'\n#                             name_1.fq.gz => name.bam\npAlignment.output = 'bam:file:{{i.fq1 | stem | stem | [:-2]}}.bam'\npAlignment.script = '''\nbwa mem -t 8 -T 0 -R <read_group> <reference> {{i.fq1}} {{i.fq2}} | \\\n    samtools view -Shb -o {{o.bam}} -\n'''\n\npBamSort = Proc(desc = 'Sort bam files.')\npBamSort.input = 'inbam:file'\npBamSort.output = 'outbam:file:{{i.inbam | basename}}'\npBamSort.script = '''\njava -jar picard.jar SortSam CREATE_INDEX=true INPUT={{i.inbam}} \\\n    OUTPUT={{o.outbam}} SORT_ORDER=coordinate VALIDATION_STRINGENCY=STRICT\n'''\n\npBamMerge = Proc(desc = 'Merge bam files.')\npBamMerge.input = 'inbam:file'\npBamMerge.output = 'outbam:file:{{i.inbam | basename}}'\npBamMerge.script = '''\njava -jar picard.jar MergeSamFiles ASSUME_SORTED=false CREATE_INDEX=true \\\n    INPUT={{i.inbam}} MERGE_SEQUENCE_DICTIONARIES=false OUTPUT={{o.outbam}} \\\n    SORT_ORDER=coordinate USE_THREADING=true VALIDATION_STRINGENCY=STRICT\n'''\n\npMarkDups = Proc(desc = 'Mark duplicates.')\npMarkDups.input = 'inbam:file'\npMarkDups.output = 'outbam:file:{{i.inbam | basename}}'\npMarkDups.script = '''\njava -jar picard.jar MarkDuplicates CREATE_INDEX=true INPUT={{i.inbam}} \\\n    OUTPUT={{o.outbam}} VALIDATION_STRINGENCY=STRICT\n'''\n```\n\nEach process is indenpendent so that you may also reuse the processes in other pipelines.\n\n## Pipeline flowchart\n```python\n# When try to run your pipline, instead of:\n#   PyPPL().start(pBamToFastq).run()\n# do:\nPyPPL().start(pBamToFastq).flowchart().run()\n```\nThen an SVG file endswith `.pyppl.svg` will be generated under current directory.\nNote that this function requires [Graphviz][13] and [graphviz for python][12].\n\nSee plugin [details][22].\n\n![flowchart][17]\n\n## Pipeline report\nSee plugin [details][23]\n\n````python\npPyClone.report = \"\"\"\n## {{title}}\n\nPyClone[1] is a tool using Probabilistic model for inferring clonal population structure from deep NGS sequencing.\n\n![Similarity matrix]({{path.join(job.o.outdir, \"plots/loci/similarity_matrix.svg\")}})\n\n```table\ncaption: Clusters\nfile: \"{{path.join(job.o.outdir, \"tables/cluster.tsv\")}}\"\nrows: 10\n```\n\n[1]: Roth, Andrew, et al. \"PyClone: statistical inference of clonal population structure in cancer.\" Nature methods 11.4 (2014): 396.\n\"\"\"\n\n# or use a template file\n\npPyClone.report = \"file:/path/to/template.md\"\n````\n\n```python\nPyPPL().start(pPyClone).run().report('/path/to/report', title = 'Clonality analysis using PyClone')\n```\n\n![report][24]\n\n## Full documentation\n[ReadTheDocs][1]\n\n\n[1]: https://pyppl.readthedocs.io/en/latest/\n[2]: https://pyppl.readthedocs.io/en/latest/api/\n[3]: https://github.com/pwwang/pyppl/\n[4]: https://img.shields.io/codacy/grade/30db7165ed6c4d7aa3261cd1f5530813.svg?style=flat-square\n[5]: https://img.shields.io/travis/pwwang/PyPPL.svg?style=flat-square\n[6]: https://img.shields.io/codacy/coverage/30db7165ed6c4d7aa3261cd1f5530813.svg?style=flat-square\n[7]: https://travis-ci.org/pwwang/PyPPL\n[8]: https://app.codacy.com/project/pwwang/PyPPL/dashboard\n[9]: https://pyppl.readthedocs.io/en/latest/CHANGELOG/\n[10]: https://img.shields.io/pypi/v/pyppl.svg?style=flat-square\n[11]: 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