Use Freyja version 2.0.0

Author: ahmig

config/README.md

@@ -141,10 +141,16 @@ All of the following variables are pre-defined in [config.yaml](/config/config.y
   - `IVAR_QUALITY`: minimum base quality for `ivar variants` (option `-q`).
   - `IVAR_FREQ`: minimum frequency threshold for `ivar variants` (option `-t`).
   - `IVAR_DEPTH`: minimum read depth for `ivar variants` (option `-m`).
-- `DEMIX`: demixing configuration:
+- `DEMIX`: demixing configuration (uses [Freyja](https://github.com/andersen-lab/Freyja), see also [its docs](https://andersen-lab.github.io/Freyja/index.html)):
+  - `PATHOGEN`: pathogen of interest for `freyja demix` (option `--pathogen`).
   - `MIN_QUALITY`: minimum quality for `freyja variants` (option `--minq`).
-  - `COV_CUTOFF`: minimum depth for `freyja demix` (option `--covcut`).
+  - `COV_CUTOFF`: minimum depth to calculate coverage for `freyja demix` (option `--covcut`).
   - `MIN_ABUNDANCE`: minimum lineage estimated abundance for `freyja demix` (option `--eps`).
+  - `CONFIRMED_ONLY`: exclude unconfirmed lineages in `freyja demix` (option `--confirmedonly`).
+  - `DEPTH_CUTOFF`: minimum depth on each site for `freyja demix` (option `--depthcutoff`).
+  - `RELAXED_MRCA`: assign clusters using relaxed (as opposed to strict) MRCA, used with `DEPTH_CUTOFF`, for `freyja demix` (option `--relaxedmrca`).
+  - `RELAXED_MRCA_THRESH`: `RELAXED_MRCA` threshold for `freyja demix` (option `--relaxedthresh`).
+  - `AUTO_ADAPT`: use error profile to set adaptive lasso penalty parameter for `freyja demix` (option `--autoadapt`).
 - `WINDOW`: sliding window of nucleotide variants per site configuration:
   - `WIDTH`: number of sites within windows.
   - `STEP`: number of sites between windows.

config/config.yaml

@@ -19,9 +19,15 @@ VC:
   IVAR_FREQ: 0.05
   IVAR_DEPTH: 30
 DEMIX:
+  PATHOGEN: "SARS-CoV-2"
   MIN_QUALITY: 20
   COV_CUTOFF: 30
   MIN_ABUNDANCE: 0.0001
+  CONFIRMED_ONLY: false
+  DEPTH_CUTOFF: 30
+  RELAXED_MRCA: false
+  RELAXED_MRCA_THRESH: 0.9
+  AUTO_ADAPT: false
 WINDOW:
   WIDTH: 1000
   STEP: 50

workflow/envs/freyja.yaml

@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - freyja==1.4.2
+  - freyja==2.0.0

workflow/rules/demix.smk

@@ -32,20 +32,30 @@ rule demix:
         variants_file = OUTDIR/"demixing"/"{sample}/{sample}_variants.tsv"
     params:
         coverage_cutoff = config["DEMIX"]["COV_CUTOFF"],
-        minimum_abundance = config["DEMIX"]["MIN_ABUNDANCE"]
+        minimum_abundance = config["DEMIX"]["MIN_ABUNDANCE"],
+        confirmed_only = "--confirmedonly " if config["DEMIX"]["CONFIRMED_ONLY"] else "",
+        depth_cutoff = config["DEMIX"]["DEPTH_CUTOFF"],
+        auto_adapt = "--autoadapt " if config["DEMIX"]["AUTO_ADAPT"] else "",
+        relaxed_mrca = "--relaxedmrca " if config["DEMIX"]["RELAXED_MRCA"] else "",
+        relaxed_mrca_thresh = config["DEMIX"]["RELAXED_MRCA_THRESH"],
+        pathogen = config["DEMIX"]["PATHOGEN"]
     output:
         demix_file = OUTDIR/"demixing"/"{sample}/{sample}_demixed.tsv"
     log:
         LOGDIR / "demix" / "{sample}.log.txt"
     shell:
-        """
-        freyja demix \
-            "{input.variants_file}" \
-            "{input.depth_file}" \
-            --eps {params.minimum_abundance} \
-            --covcut {params.coverage_cutoff} \
-            --output {output.demix_file} >{log} 2>&1
-        """
+        "freyja demix "
+        "{input.variants_file:q} "
+        "{input.depth_file:q} "
+        "--eps {params.minimum_abundance} "
+        "--covcut {params.coverage_cutoff} "
+        "--depthcutoff {params.depth_cutoff} "
+        "{params.confirmed_only}"
+        "{params.auto_adapt}"
+        "{params.relaxed_mrca}"
+        "--relaxedthresh {params.relaxed_mrca_thresh} "
+        "--output {output.demix_file} "
+        ">{log} 2>&1"
 
 
 rule summarise_demixing: