Elusive syntax error in Snakefile

Question

[Giuseppe Giovanni]

Hi,

I'm quite new to snakemake and was trying to write a little workflow to analyze some nanopore data. However, it keeps returning an invalid syntax error caused by this rule

rule alignment:
    input:
        "{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz"
    output:
        "{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam",
        "{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai"
    resources:
        partition: "EPYC"
        runtime: 5760
        mem_mb: 200000
        cpus_per_task: 20
    conda:
        "{env_file}"
    params:
        ngmlr_args="-t 20 -r /fast/burlo/fcrudele/resources/hgRef/GRCh38.p13/no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -x ont"
    message: """ ngmlr Alignment """
    shell:
        """
        ngmlr {params.ngmlr_args} -q {input}  | samtools view -b /dev/stdin |  samtools sort -@ 20 -o {output[0]} &&
        samtools index -@ 20 -b -o {output[1]}
        """

The syntax error is caused by the first line after the "output:" directive, but I'm unable to see it. What would be the problem here ?

Thanks in advance!

[Ram]

EDIT: Maybe the lack of commas in the resources part is the problem.

---

What is the exact error being shown?

Can you also pass the above rule text though cat -A to show all invisible characters please?

[Giuseppe Giovanni]

Thank you for the suggestions! I've added the commas in the resources section, but it returns the same error as before:

SyntaxError in file /orfeo/cephfs/home/burlo/nardone/pipelines/minION_workflow/Snakefile, line 91: invalid syntax (Snakefile, line 91)

Using cat -A as suggested shows this:

rule alignment:$
    input:$
        "{base_out}/2.TRIMMING/{sample}.trimmed_and_clean.fastq.gz"$
    output:$
        "{base_out}/3.ALIGNMENT/{sample}.ngmlr.bam",$
        "{base_out}/3.ALIGNMENT/{sample}.ngmlr.bai"$
    resources:$
        partition: "EPYC",$
        runtime: 5760,$
        mem_mb: 200000,$
        cpus_per_task: 20$
    conda:$
        "{env_file}"$
    params:$
        ngmlr_args="-t 20 -r /fast/burlo/fcrudele/resources/hgRef/GRCh38.p13/no_alt/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -x ont"$
    message: """ ngmlr Alignment """$
    shell:$
        """$
        ngmlr {params.ngmlr_args} -q {input}  | samtools view -b /dev/stdin |  samtools sort -@ 20 -o {output[0]} &&$
        samtools index -@ 20 -b -o {output[1]}$
        """$

Line 91 is the first line after the output directive in my snakefile

[vkkodali_ncbi]

Don't you need commas after each resource in resources?

[Giuseppe Giovanni]

Thanks for the advice!

I've tried to add the commas in the resources section but it returns the same error as before:

SyntaxError in file /orfeo/cephfs/home/burlo/nardone/pipelines/minION_workflow/Snakefile, line 91: invalid syntax (Snakefile, line 91)

with line 91 being the first line after the output directive

[dariober]

Maybe "{env_file}" should be something like f"{env_file}" but I doubt that would be a syntax error anyway. In some old versions of snakemake there was a bug in reporting the line number of errors. If possible, post the snakefile at least up to rule alignment.

Answer 1

[Giuseppe Giovanni]

I've finally been able to spot what is the problem. In the documentation there's this example:

rule:
input: ...
output: ...
resources:
    partition: <partition name>
    runtime: <some number>

However, apart from the missing commas, resources need to be specified with the resource=<resource> format. So, I've just corrected the resources part as:

resources:
        partition="EPYC",
        runtime=5760,
        mem_mb=200000,
        cpus_per_task=20

And like this it seems to work. Thanks everyone for their responses and suggestions!

[Ram]

Wonderful that you figured it out! Please accept your answer to provide closure to the post.