Unable to run with updated WILDCARD pattern to match my sample IDs

[shlokanegi]

Hi. I don't have experience running Snakemake, so forgive me if it's a rookie mistake on my end.

I am trying to run MeOW on a set of patient samples, sequenced with nanopore. My sample IDs are of the format "M11AB, M11CD, etc..." So, I made changes to the Snakefile to match the pattern - SAMPLE="M\d{2}[A-Z]{2}". I followed all steps mentioned in the README. Below is the screenshot of the "blood_5mc_bam_files.tsv" file, consisting of bamfile paths.

This is what I run - snakemake --use-conda --cores 32

Error message

Building DAG of jobs...
MissingInputException in rule all in file /path/to/home/methylation/MeOW/workflow/Snakefile, line 12:
Missing input files for rule all:
    affected files:
        results/Nothing_meow_results/Nothing.beta.dmr.html

Please let me know if you need any other information. Appreciate any help! Thank You!!

[shlokanegi]

Attaching the config.yaml file here -

CPGISLANDLOC: "resources/positions"
# path to named cpg region file
CPGREGIONS : "resources/named.cpgIslands.hg38.sorted.bed"

#paths to rust executables
RUSTANNOTATE : "workflow/scripts/./intervalAssign"

# default region file
DEFAULTREGION : "resources/allChrom.bed"

#Files and paths needed for annotation
NAMEDCPGS : "resources/cpgIslands.sorted.named.core.tsv"
NAMEDGENES : "resources/all.sorted.targets.intervals.tsv"

single_target : "Nothing"

LC_ALL : C
samples: config/blood_5mc_bam_files.tsv
targetfile: config/targets.txt
control_metadata: config/blood_5mc_control_metadata.csv
metadata: config/test_metadata.csv
minimum_control_CpGs: 4000000
methylation_type: "5mc" # 5mc, 5hmc5mc_ignore, 5hmc5mc_bayes

[cccosmic]

Hi,

I am trying to run something similar and I am getting the same error. Were you able to find what the problem was?

Thank you

[Madelinehazel]

Hello, I'm experiencing the same issue, even when I try to do a dry run with the example config files. Any help would be much appreciated! Thanks, Madeline