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Merged
johnlees merged 1 commit into from
Feb 3, 2026
Merged

Pass freq param to ska #29

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19 changes: 15 additions & 4 deletions README.md
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Expand Up @@ -51,7 +51,20 @@ In addition to the above, for each strain:
- Use [bactdating](https://github.com/xavierdidelot/BactDating) to make timed trees.
- Use [transphylo](https://github.com/xavierdidelot/TransPhylo) to infer transmission events on these timed trees.

This requires a `transmission_metadata.csv` file containing sampling times, see the PopPIPE configuration section below for a description of its format.
This requires a `transmission_metadata.csv` file containing sampling times, this file should look like this:
```
Name,Date
001334,2001
279388,2001
5Z52R,2007
```
Where the sample names match the PopPUNK analysis, followed by a date.

Please note that bactDating parses the dates using:
```r
tryFormats = c("%Y-%m-%d", "%Y/%m/%d", "%Y")
```
So your dates should be in a compatible format, usually at the same resolution (e.g. all just years)

For an example of this analysis, please find data at [10.6084/m9.figshare.28495571](https://dx.doi.org/10.6084/m9.figshare.28495571).
Input files and config file are in `input/` and the pipeline output after running `snakemake transmission --cores 4` is
Expand Down Expand Up @@ -122,9 +135,7 @@ in `config.yml` which lists the sampling dates. The run the transmission target:
snakemake transmission
```

## Usage example

TODO
Ensure dates are formatted consistently (see above).

## Config file

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6 changes: 3 additions & 3 deletions Snakefile
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Expand Up @@ -137,9 +137,10 @@ rule ska_align:
log:
"logs/ska_align_{strain}.log"
params:
prefix="output/strains/{strain}/align"
prefix="output/strains/{strain}/align",
min_freq=config['ska']['freq_filter']
shell:
"ska align -v --filter no-const --no-gap-only-sites {input.skf} > {output.alignment} 2> {log}"
"ska align -v --min-freq {params.min_freq} --filter no-const --no-gap-only-sites {input.skf} > {output.alignment} 2> {log}"

# ska for mapping (needed for gubbins)
rule ska_map:
Expand Down Expand Up @@ -174,7 +175,6 @@ rule iq_tree:
mode=config['iqtree']['mode'],
model=config['iqtree']['model'],
prefix="output/strains/{strain}/besttree.unrooted"

threads:
4
script:
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4 changes: 2 additions & 2 deletions config.yml
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Expand Up @@ -16,7 +16,7 @@ ska:
fastq_cov: 4
kmer: 31
single_strand: false
freq_filter: 0.9
freq_filter: 0.9 # only used in ska align step

# IQ-TREE options
iqtree:
Expand All @@ -37,7 +37,7 @@ mandrake:

# Microreact title, and your contact details
microreact:
name: Listeria PopPIPE
name: PopPIPE run
website: https://www.poppunk.net
email: poppunk@poppunk.net
api_token: a1b2c3d4 ## see https://docs.microreact.org/api/access-tokens
Expand Down
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