{"id":25905410,"url":"https://github.com/stevekm/skidsteer","last_synced_at":"2025-07-05T09:04:48.471Z","repository":{"id":94518058,"uuid":"82251804","full_name":"stevekm/SkidSteer","owner":"stevekm","description":"Task \u0026 workflow pipeline framework","archived":false,"fork":false,"pushed_at":"2017-08-01T04:16:53.000Z","size":2942,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-06-10T21:49:28.460Z","etag":null,"topics":["bioinformatics","bioinformatics-pipeline","pipeline","pipeline-framework"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/stevekm.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2017-02-17T03:12:00.000Z","updated_at":"2023-06-12T15:45:03.000Z","dependencies_parsed_at":"2023-07-28T07:45:27.849Z","dependency_job_id":null,"html_url":"https://github.com/stevekm/SkidSteer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/stevekm/SkidSteer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FSkidSteer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FSkidSteer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FSkidSteer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FSkidSteer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/stevekm","download_url":"https://codeload.github.com/stevekm/SkidSteer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/stevekm%2FSkidSteer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263715325,"owners_count":23500241,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bioinformatics-pipeline","pipeline","pipeline-framework"],"created_at":"2025-03-03T05:15:06.567Z","updated_at":"2025-07-05T09:04:48.466Z","avatar_url":"https://github.com/stevekm.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SkidSteer \n`SkidSteer` is a Python class-based framework for data analysis workflows, designed with bioinformatic pipelines in mind and inspired by the [Ruffus](http://www.ruffus.org.uk/) [package](https://pypi.python.org/pypi/ruffus). \n\n![skidsteer](https://user-images.githubusercontent.com/10505524/28391490-44193b9c-6cac-11e7-96bd-d27152a6cb67.jpeg)\n\n# Classes\n\n## Base Classes\n\nThese classes are defined in `base_classes.py`\n\n### `PipelineTask`\n\nThis class represents a task to be performed by the pipeline. It has attributes and methods that set the task's input \u0026 output directories and files. \n\n### `ShellTask`\n\nA `PipelineTask` which ultimately invokes a command to run on the shell, using a wrapper to the Python `subprocess` package. \n\n### `PythonTask`\n\nA `PipelineTask` which can hold custom Python code. \n\n## User Defined Classes\n\nIn order to use `SkidSteer`, the user should create subclasses of `ShellTask` and `PythonTask` for their pipeline tasks. These should be held in the `pipeline_classes.py` file. See [pipeline_classes.py](https://github.com/stevekm/SkidSteer/blob/master/pipeline_classes.py) for examples.\n\n# Methods\n\nSome notable object methods include:\n\n- `build_command`: All classes should have a `build_command` method, which is used to build a shell command to run (`ShellTask`) or should contain custom Python code to run (`PythonTask`). This method should be filled in by the user.\n\n- `run`: All classes will come with the `run` method, which invokes `build_command` and runs the generated command, if applicable. The user should not modify this method. \n\n# Pipeline\n\nThe complete list of tasks to be run in the pipeline are held in `pipeline.py`. Task objects should be created in the `build_pipeline_task_list` function, and added to a `task_list` in the desired order of completion. The `run_pipeline` function will evaluate and run each task in the list. \n\n# Design Goals\n\nThe following goals were considered in the development of the `SkidSteer` package:\n\n- modularity of adding and managing tasks\n- linear pipeline task completion\n- standardized input/output file mapping (as much as possible)\n- room for user to implement own methods \u0026 techniques inside of tasks\n- object oriented system\n- linear object class inheritance (no diamond inheritance or multiple inheritance)\n- Python 2.7/3+ compatible\n- **the main pipeline script (e.g. `pipeline.py`) should be easy to read and follow; sequester complex program logic in external modules (e.g. `base-classes.py`, etc.)**\n\nThe following aspects were actively avoided in the creation of `SkidSteer`:\n\n- complex branching of inheritance or pipeline tasks\n- excessively deep inheritance; currently at 2 base levels + 1 user level, try not to go any deeper\n\n# Example Output\n\nThe following output can been seen by running the provided example [pipeline](https://github.com/stevekm/SkidSteer/blob/4c8a9100e89f48b77e866a13865f82c206ce5523/pipeline.py)\n\n```\n$ ./pipeline.py\n--------------------\nRunning Pipeline\n\nSample ID is: test2\n\n\n--------------------\nNow running task: printfoo\n\nCommand is:\n\n\n\n\necho foo\n\n\nfoo\n--------------------\nNow running task: fastqc\n\nCommand is:\nmodule load fastqc/0.11.4\nfastqc --threads 4 --nogroup --outdir output/fastqc input/test2.fastq\n/bin/sh: module: command not found\nStarted analysis of test2.fastq\nAnalysis complete for test2.fastq\n--------------------\nNow running task: bowtie2\n\nCommand is:\nbowtie2 --local -x \"~/ref/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome\" -q -U input/test2.fastq --threads 1 | samtools view -@ \"1\" -Sb1 - | samtools sort -m 2G -@ \"1\" - -o  \"output/bowtie2/test2.bam\"\nsamtools index \"output/bowtie2/test2.bam\"\n10 reads; of these:\n  10 (100.00%) were unpaired; of these:\n    0 (0.00%) aligned 0 times\n    9 (90.00%) aligned exactly 1 time\n    1 (10.00%) aligned \u003e1 times\n100.00% overall alignment rate\n\n--------------------\nNow running task: bamToBedgraph\n\nCommand is:\nexport LC_COLLATE=C\nbedtools genomecov -ibam \"output/bowtie2/test2.bam\" -g \"data/hg19.chrom.sizes_full.txt\" -bg \u003e \"output/bamToBedgraph/test2.bedgraph\"\nsort -k1,1 -k2,2n output/bamToBedgraph/test2.bedgraph \u003e output/bamToBedgraph/tmp \u0026\u0026 /bin/mv output/bamToBedgraph/tmp output/bamToBedgraph/test2.bedgraph\n\n--------------------\nNow running task: bamToBed\n\nCommand is:\nexport LC_COLLATE=C\nbamToBed -i output/bowtie2/test2.bam \u003e output/bamToBed/test2.bed\nsort -k1,1 -k2,2n output/bamToBed/test2.bed \u003e output/bamToBed/tmp \u0026\u0026 /bin/mv output/bamToBed/tmp output/bamToBed/test2.bed\n\n--------------------\nNow running task: bedToBigBed\n\nCommand is:\nbedToBigBed \"output/bamToBed/test2.bed\" \"data/hg19.chrom.sizes_full.txt\" \"output/bedToBigBed/test2.bigbed\"\npass1 - making usageList (8 chroms): 1 millis\npass2 - checking and writing primary data (10 records, 6 fields): 2 millis\n\n--------------------\nNow running task: bedgraphToBigWig\n\nCommand is:\nbedGraphToBigWig \"output/bamToBedgraph/test2.bedgraph\" \"data/hg19.chrom.sizes_full.txt\" \"output/bedgraphToBigWig/test2.bw\"\n\n--------------------\nNow running task: python-task\n\nThis is some Python code\n--------------------\nNow running task: txt2fastq\n\nCommand is:\necho \"In this step I am going to convert a file\"\nIn this step I am going to convert a file\n```\n\nOutput can be seen here:\n\n```\n$ tree output\noutput\n|-- bamToBed\n|   `-- test2.bed\n|-- bamToBedgraph\n|   `-- test2.bedgraph\n|-- bedToBigBed\n|   `-- test2.bigbed\n|-- bedgraphToBigWig\n|   `-- test2.bw\n|-- bowtie2\n|   |-- test2.bam\n|   `-- test2.bam.bai\n|-- fastqc\n|   |-- test2_fastqc.html\n|   `-- test2_fastqc.zip\n|-- printfoo\n|-- python-task\n`-- txt2fastq\n```\n\n# Why `SkidSteer`?\nBecause the best pipeline is one you built yourself.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fskidsteer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstevekm%2Fskidsteer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstevekm%2Fskidsteer/lists"}