CODEWITHSUNDEEP
makefilesnakemake
user378147
user378147

Reputation:

Snakemake: name rule instead of target file

Here is a short example from the advanced section of snakemake tutorial:

rule bwa_map:
input:
    "data/genome.fa",
    lambda wildcards: config["samples"][wildcards.sample]
output:
    "mapped_reads/{sample}.bam"
threads: 8
shell:
    "bwa mem -t {threads} {input} | samtools view -Sb - > {output}"

Now lets say that I wrote this rule months ago and I don't remember the output file name. My understanding is that I cannot run snakemake by invoking the rule name because this would lead to an error:

$ snakemake bwa_map
InputFunctionException in line 9 of Snakefile:
AttributeError: 'Wildcards' object has no attribute 'sample'
Wildcards:

$

First, I don't understand why snakemake cannot use the lambda function to deduce input files from the configuration file as it is quite clear that I refer to the "samples" section.

Second, is there a workaround to this? Because it is very easy to do with good old Makefile to just use an old Makefile and run the same bwa_map rule by typing something like

$ make bwa_map INPUT=data/samples/A.fastq

Thanks in advance for your help. Benoist

Upvotes: 4

Views: 2244

Answers (1)

Johannes Köster
Johannes Köster

Reputation: 1947

If you specify a rule name as a target and that rule contains wildcards, Snakemake can't know what values to use for the wildcards. This can only be determined from a concrete output file in this case. This output file can come from a downstream rule, e.g. a real ´all´ target at the top of the Snakefile, or by providing it directly at the command line.

However if you have a proper target rule at the top of the Snakefile, there is the --until flag, which allows you to execute your workflow only until a given rule.

Regarding your make example, I am not aware of this functionality. Can you point me to the docs about this? I might add something similar to Snakemake as well.

Please also note that I just improved the error message for this case in the development version of Snakemake. It is now more informative and explains the issue.

Upvotes: 1

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