Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/cwl in rule

Question

[msimmer92]

There is some problem with my samtools_dup rule.

It says "SyntaxError in line 201 of /data/mypipeline.smk: No rule keywords allowed after run/shell/script/wrapper/cwl in rule samtools_dup. (mypipeline.smk, line 201)".

If I google the error, I found that a person says that, in their code, might be that he placed the "log:" after the "shell:" (and that the shell should be the last thing in each rule), but in my code that is not the case. In many other forums I saw people posting it but no answer was recorded. I am not sure where else this mistake can be... any thoughts? Thank you !

Here I post the code for you to take a look.

dup_fun = "rmdup"
# Mark or remove duplicates with Samtools
if ( mrDup == "mark" or mrDup == "rm" ):
    rule samtools_dup:
        input: f'{bamDir}' + '/{sample}_sort.bam')
        params: fun = "rmdup"
        output: protected(f'{dupDir}' + "/" + f'{mrDup}dup.bam')
        shell: "samtools {params.fun} -s {input} {output}"

Edited: when I delete this rule from the pipeline, the error goes away with it. What comes next in the code is my bigwig rule:

# Bigwig with Deeptools bamCoverage
if ( bigWig == "yes" ):
    rule bigwig:
        input:
            bam = f'{bamDir}' + '/{sample}.bam',
            bai = f'{bamDir}' + '/{sample}.bai'
        output: f'{bwDir}' + '/{sample}.bw'
        params:
            xtnd = bwXtnd ,
            bs = binSize ,
            nrm = normBW ,
            effgs = effGS ,
            bl = f'-bl {blBed}'
        conda:
            "envs/deeptools.yaml"
        threads: maxThreads
        shell:
            "bamCoverage -b {input.bam} -bs {params.bs} --normalizeUsing {params.nrm} --effectiveGenomeSize {params.effgs} -o {output} {params.xtnd} {params.bl}"

[Devon Ryan]

What comes after the shell: line? Most likely you have an indentation problem later, since what you posted looks fine.

[msimmer92]

There is an empty line (two enters, from the end of the shell line) and then what you see in the second code panel (the bigwig rule - I added it now to this question). When I delete the samtools_dup rule, the code works. I'll try to put it again and double-check indentations, but the next rule's first two lines don't have any (the comment and the if clause). (ps: this is for chip-seq data)

[Devon Ryan]

My only guess is that there's a single space missing somewhere, since otherwise everything looks fine to me.

Answer 1

[msimmer92]

Dmitry Kuzminov solved it in StackOverflow. I share the answer here, in case someone has the same doubt! It seems there is an extra parenthesis at the end of the "input" line in the samtools_dup rule. I honestly didn't spot it, and also the error message made me think the problem wasn't there but around the "shell" statement.

https://stackoverflow.com/questions/60914204/snakemake-syntaxerror-no-rule-keywords-allowed-after-run-shell-script-wrapper-c/60924399#60924399