Snakemake - Revision history

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2018-02-24T00:59:51Z

Projects

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	Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake		Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake

			Snakemake wrappers for common bioinformatics components: https://snakemake-wrappers.readthedocs.io/en/stable/

	==Documentation==		==Documentation==

2018-02-23T01:12:19Z

Walkthrough Example

← Older revision		Revision as of 01:12, 23 February 2018
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	Walkthrough example with a non-trivial bioinformatics workflow called dahak-flot: [[Snakemake/DahakFlot]]		Walkthrough example with a non-trivial bioinformatics workflow called dahak-flot: [[Snakemake/DahakFlot]]

			==Strategies and Patterns==

			Stragies for designing Snakemake files and patterns for complex workflows: [[Snakemake/Patterns]]

	=Links=		=Links=

2018-02-22T05:12:17Z

2018-02-22T01:57:00Z

Walkthrough Example

← Older revision		Revision as of 01:57, 22 February 2018
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	==Walkthrough Example==		==Walkthrough Example==

	Walkthrough example with a non-trivial bioinformatics workflow: [[Snakemake/~~Dahak~~]]		Walkthrough example with a non-trivial bioinformatics workflow called dahak-flot: [[Snakemake/DahakFlot]]

	=Links=		=Links=

2018-02-22T01:56:23Z

← Older revision		Revision as of 01:56, 22 February 2018
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	"somecommand {input} {output}"		"somecommand {input} {output}"
	</pre>		</pre>

			==Walkthrough Example==

			Walkthrough example with a non-trivial bioinformatics workflow: [[Snakemake/Dahak]]

	=Links=		=Links=

2018-02-22T01:33:06Z

Documentation

← Older revision		Revision as of 01:33, 22 February 2018
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	Rules: https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#targets		Rules: https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#targets

			Setup/tutorial: https://snakemake.readthedocs.io/en/stable/tutorial/setup.html#step-1-installing-miniconda-3

	==Examples==		==Examples==

2018-02-22T01:32:56Z

Links

← Older revision		Revision as of 01:32, 22 February 2018
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	Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake		Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake

			==Documentation==

			Rules: https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#targets

	==Examples==		==Examples==

2018-02-10T19:16:30Z

How It Works

← Older revision		Revision as of 19:16, 10 February 2018
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	A rule in snakemake is a mapping from an input file to an output file.		A rule in snakemake is a mapping from an input file to an output file.

	~~<pre>~~
	~~rule targets:~~
	~~input:~~
	~~"plots/dataset1.pdf",~~
	~~"plots/dataset2.pdf"~~
	~~</pre>~~

	<pre>		<pre>
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	"somecommand {input} {output}"		"somecommand {input} {output}"
	</pre>		</pre>




	=Links=		=Links=

2018-02-10T19:04:49Z

Examples

← Older revision		Revision as of 19:04, 10 February 2018
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	Amplicon trimming workflow using a short snakemake file: https://github.com/snakemake-workflows/accel-amplicon-trimming/blob/master/Snakefile		Amplicon trimming workflow using a short snakemake file: https://github.com/snakemake-workflows/accel-amplicon-trimming/blob/master/Snakefile

			Both are listed on the snakemake workflows repo page: https://github.com/snakemake-workflows/docs

	=Flags=		=Flags=

2018-02-10T19:04:27Z

Links

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 pip install snakemake
 </pre>
 =Links=
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 A SingleCell RNASeq pre-processing pipeline built on snakemake: https://github.com/Hoohm/dropSeqPipe/blob/master/Snakefile
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