KeyError in line 16 of hAMRonization_workflow/rules/staramr.smk: 'pointfinder'

[SvetlanaUP]

Hi, after running:

git clone https://github.com/pha4ge/hAMRonization_workflow
conda env create -n hamronization_workflow --file envs/hamronization_workflow.yaml
conda activate hamronization_workflow
snakemake --configfile config/config.yaml --use-conda --jobs 2 --use-singularity --singularity-args "-B $PWD:/data"

I'm getting the error:
KeyError in line 16 of .../hAMR/test/hAMRonization_workflow/rules/staramr.smk:
'pointfinder'
File ".../hAMR/test/hAMRonization_workflow/Snakefile", line 75, in
File ".../hAMR/test/hAMRonization_workflow/rules/staramr.smk", line 16, in

After deleting "include: "rules/staramr.smk"" in the Snakefile, it seems ok but then getting:
Building DAG of jobs...
MissingInputException in line 19 of .../hAMR/test/hAMRonization_workflow/rules/ariba.smk:
Missing input files for rule run_ariba:
data/test/SAMEA6634591/ERR4008003_R1.fastq.gz
data/test/SAMEA6634591/ERR4008003_R2.fastq.gz

One more question: if I have only assembly, in isolate_list.txt info on reads, read1 and read2 can be just left blank?

Thanks,
Svetlana

[fmaguire]

Staramr pointfinder error

Ah yes, I'd fixed that first issues months back but totally forgotten to push. That issue will be resolved as of #82d34cc

Missing input files for ariba

The config needs changed to point to your own isolate_list.txt as that is the error when its looking for the test data but they haven't been downloaded yet.

Optional read-based methods

Currently read and contig based methods are run on all samples so no fields can be left blank.
This workflow was initially just created as a proof of concept rather than an actual production workflow. I'm currently just going through and updating the tools/envs and improving containerisation using the latest snakemake features, I'll add an optional flag to the config file to have the workflow not run read-based methods.