No results generated after running the Snakemake workflow

[Vini2]

Hello!

I followed the steps provided in the README to run the workflow for my data but no results were generated. I only get the following output and there are no other errors.

(snakemake) username@x111:MEDUSA-main$ snakemake --cores
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 32
Rules claiming more threads will be scaled down.
Job stats:
job      count    min threads    max threads
-----  -------  -------------  -------------
all          1              1              1
total        1              1              1

Select jobs to execute...

[Sun Jan 29 14:19:32 2023]
localrule all:
    jobid: 0
    reason: Rules with neither input nor output files are always executed.
    resources: tmpdir=/tmp

[Sun Jan 29 14:19:32 2023]
Finished job 0.
1 of 1 steps (100%) done
Complete log: .snakemake/log/2023-01-29T141932.335381.snakemake.log

I executed the snakemake --cores command from where the Snakefile is and ensured that my raw FASTQ files are in the Pipeline/data/raw folder. Also I made sure that my reads end with the suffixes _1.fast and _2.fastq.

Can you please help me figure this out?

Thank you!

[gleisonm]

Hello @Vini2,

I had a look at this lines from the snakefile:

IDs = glob_wildcards(join(inputDIR,
    "{id, [A-Za-z0-9]+}{suffix, (_[1-2])?}.fastq"))

It appears that the input file names are restricted from including special characters, except for the underscore from _1.fastq or _2.fastq.

I hope this help on what you were facing. If not, don't hesitate to comment on this issue.

Wishing you the best of luck.