Snakemake/DahakFlot - Revision history

Admin: Replacing charlesreid1.com:3000 with git.charlesreid1.com

2019-10-09T03:53:05Z

Replacing charlesreid1.com:3000 with git.charlesreid1.com

← Older revision		Revision as of 03:53, 9 October 2019
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	Main repository:		Main repository:
	* https://charlesreid1.com~~:3000~~/dotfiles/dahak-flot		* https://git.charlesreid1.com/dotfiles/dahak-flot
	* https://github.com/charlesreid1/dahak-flot		* https://github.com/charlesreid1/dahak-flot

2018-02-22T08:34:19Z

Expanding Patterns to Lists of Files

← Older revision		Revision as of 08:34, 22 February 2018
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	Suppose we want to write a rule that, for its input and output files, should match a wildcard expression and turn it into a list of files.		Suppose we want to write a rule that, for its input and output files, should match a wildcard expression and turn it into a list of files.

			As an example:

			Start by defining a list of variables at the top of the file:

			<pre>
			SAMPLES = ["A", "B"]
			</pre>

			Now, use the expand function to feed in a string with a special formatting code, and a keyword argument:

			<pre>
			expand("sorted_reads/{sample}.bam", sample=SAMPLES)
			</pre>

			===Example Expand Rule===

			Here is an example expand rule:

			<pre>
			rule bcftools_call:
			input:
			fa="data/genome.fa",
			bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
			bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
			output:
			"calls/all.vcf"
			shell:
			"samtools mpileup -g -f {input.fa} {input.bam} \| "
			"bcftools call -mv - > {output}"
			</pre>

	=Flags=		=Flags=

2018-02-22T07:03:45Z

Flags

← Older revision		Revision as of 07:03, 22 February 2018
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	3		3
	</pre>		</pre>

			=More Complicated Operations=

			==Expanding Patterns to Lists of Files==

			Suppose we want to write a rule that, for its input and output files, should match a wildcard expression and turn it into a list of files.



	=Flags=		=Flags=

2018-02-22T06:59:49Z

Executing First Rule

← Older revision		Revision as of 06:59, 22 February 2018
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	This creates a folder with data in it, and an environment.yaml file for conda.		This creates a folder with data in it, and an environment.yaml file for conda.

	===~~Executing~~ First Rule===		===Running the First Rule===

	Unlike with Makefiles, Snakefile rules are executed based on their output files. So, if we want to execute the rule bwa_map, we look at the output file:		Unlike with Makefiles, Snakefile rules are executed based on their output files. So, if we want to execute the rule bwa_map, we look at the output file:

2018-02-22T06:59:32Z

Adding a Third Rule

← Older revision		Revision as of 06:59, 22 February 2018
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	</pre>		</pre>

	Now we have three rules that will run sequentially (bwa_map -> samtools_sort -> samtools_index) so long as we ask for the output file of the last rule, samtools_index:		Now we have three rules that will run sequentially (bwa_map -> samtools_sort -> samtools_index) so long as we ask for the output file of the last rule, samtools_index.

			===Running the Third Rule===

			To run the third rule:

	<pre>		<pre>

2018-02-22T06:58:08Z

More Snakefile Rules

@@ Line 215: / Line 215: @@
 Note that the rules are chained together because the output of bwa_map is the same as the input of samtools_sort. Also note that the two strings in the shell command are not separated by a comma so they are concatenated.
 Again, Snakemake is focused on the output files you want, so in this case we will let sample be A and B, which requires us to have data/samples/A.fastq and data/samples/B.fastq in place. Then ask for the output of samtools_sort:
@@ Line 228: / Line 230: @@
 <pre>
 snakemake sorted_reads/A.bam sorted_reads/B.bam
 </pre>

2018-02-22T05:22:20Z

More Snakefile Rules

@@ Line 216: / Line 216: @@
 Note that the rules are chained together because the output of bwa_map is the same as the input of samtools_sort. Also note that the two strings in the shell command are not separated by a comma so they are concatenated.
-Again, Snakemake is focused on the output files you want, so in this case we will let sample be A and B, which requires us to have data/samples/A.fastq and data/samples/B.fastq in place.
+Again, Snakemake is focused on the output files you want, so in this case we will let sample be A and B, which requires us to have data/samples/A.fastq and data/samples/B.fastq in place. Then ask for the output of samtools_sort:
 =Flags=

2018-02-22T05:19:31Z

More Snakefile Rules

← Older revision		Revision as of 05:19, 22 February 2018
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	</pre>		</pre>

	Note that the rules are chained together because the output of bwa_map is the same as the input of samtools_sort.		Note that the rules are chained together because the output of bwa_map is the same as the input of samtools_sort. Also note that the two strings in the shell command are not separated by a comma so they are concatenated.

	~~Also note that~~ the ~~two strings~~ in ~~the shell command are not separated by a comma so they are concatenated~~.		Again, Snakemake is focused on the output files you want, so in this case we will let sample be A and B, which requires us to have data/samples/A.fastq and data/samples/B.fastq in place.

	=Flags=		=Flags=

2018-02-22T05:18:32Z

First Snakefile Rule

@@ Line 189: / Line 189: @@
 snakemake -np mapped_reads/{A,B}.bam
 </pre>
 =Flags=

2018-02-22T05:14:08Z

Executing the Rule

← Older revision		Revision as of 05:14, 22 February 2018
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	This creates a folder with data in it, and an environment.yaml file for conda.		This creates a folder with data in it, and an environment.yaml file for conda.

	==Executing ~~the~~ Rule==		===Executing First Rule===

	Unlike with Makefiles, Snakefile rules are executed based on their output files. So, if we want to execute the rule bwa_map, we look at the output file:		Unlike with Makefiles, Snakefile rules are executed based on their output files. So, if we want to execute the rule bwa_map, we look at the output file: