Inspection: trailing comment at the end of Snakefile about snakecharm HOT 13 CLOSED

Just to clarify: Is the correct behavior that this should not be an error?

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@olegs Is it really introduce an error?

I've tried

rule all:
    output:
        foo=touch('foo'),

and

rule all:
    output:
        foo=touch('foo'),
    params:
        threads=1

both works ok using snakemake 5.4.0

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Ok, so I think what @olegs may be trying to say is that the trailing commas are marked red in Pycharm, but trailing commas are actually fine for the snakemake interpreter. In any case, I certainly see this, and I find it a minor annoyance.

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To clarify, given the following rule definition:

rule my_rule:
    input: 'my_input.file',
    output: 'my_output.file'
    shell: 'echo hi world'

In the above example, output: is underlined in red. The tooltip reads "Unresolved reference 'output'"

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@winni2k Thank you for the test case, indeed SnakeCharm plugin highlights the trailing commas as red when they are on the same line as a section name, see the screenshot: error on 4-th line, not on 3-rd

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Fixed, will be available in next release 0.4.x

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SnakeCharm doesn't warn of trailing comma for code which fails on runtime

# $ source activate snakemake
# $ snakemake  --use-conda --cores 8

configfile: "config.yaml"
workdir: config['work_dir']

include: "step1_raw_qc.smk"
include: "step2_alignment.smk"
include: "step3_reads_coverage.smk"

rule all:
    input:
         rules.step1_raw_qc_results.input,
         rules.step2_alignment_results.input,
         # rules.step3_reads_coverage_results.input

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But snakemake doesn't fail if I add empty line at the end of file

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I don't think this is relevant to the comma question as both of these inputs fail with a syntax error on my machine:

rule all:
     input:
         'bla'
	 # bla2

rule all:
     input:
         'bla',
	 # bla2

Perhaps this is a bug in the snakemake interpreter? It appears the comment is necessary in order for this to be called a syntax error.

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This also fails:

rule all:
     input:
         'bla'

# bla2

I think it must be something to do with a file ending in a commented line?

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@winni2k Yes, looks like some bug in snakemake

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Thanks for fixing this!

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