Add the possibility to use the --resfinder_species parameter outside the YAML file to set a global value for all samples described in the YAML. Which can then be overwritten if a specific sample has another value for it in samplesheet.
It will work like this, for example:
--resfinder_species Klebsiella will set all samples from the YAML as Klebsiella.
However, if the samplesheet is like this:
samplesheet:
- id: sample_1
illumina:
- sample_1/1.fastq
- sample_1/2.fastq
nanopore: sample_1/ont.fastq
resfinder: Escherichia coli
- id: sample_2
assembly: sample_2/assembly.fasta
- id: sample_3
nanopore: sample_3/ont.fastq
fast5: sample_3/fast5_passIt will run sample 2 and 3 as the global value "Klebsiella" and sample 1 will be run as "Escherichia coli" since it overwrites the global definition by setting a value inside the YAML.
Add the possibility to use the
--resfinder_speciesparameter outside the YAML file to set a global value for all samples described in the YAML. Which can then be overwritten if a specific sample has another value for it in samplesheet.It will work like this, for example:
--resfinder_species Klebsiellawill set all samples from the YAML as Klebsiella.However, if the samplesheet is like this:
It will run sample 2 and 3 as the global value "Klebsiella" and sample 1 will be run as "Escherichia coli" since it overwrites the global definition by setting a value inside the YAML.