update example config.yaml

example_config.yaml

@@ -32,6 +32,10 @@ viral_reference_feature_coords: 'data/MN908947.3.gff3'
 run_breseq: False
 # Used as --reference argument to 'breseq'
 breseq_reference: 'data/MN908947.3.gbk'
+# Used as --polymorphism-minimum-variant-coverage-each-strand, --polymorphism-frequency-cutoff arguments
+# Parameters needed to determine thresholds for minor variant detection
+polymorphism_variant_coverage: 2
+polymorphism_frequency: 0.05
 
 # run freebayes for variant and consensus calling (as well as ivar)
 run_freebayes: True
@@ -73,7 +77,7 @@ pango-designation:
 pangolin-data:
 
 # Versions for Nextclade (software & datasets)
-# nextclade: Software version. Input should use numbers only (i.e., 2.14.0)
+# nextclade: Software version. Input should use numbers only (i.e., 2.14.0). Must be >=1.3.0.
 # nextclade-data: The nextclade dataset tag. Refer to available nextclade datasets. Accepted tag format is 'YYYY-mm-ddTHH:MM:SSZ'
 # Be as specific as possible with the desired dataset tag. Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS). SIGNAL will automatically adjust between v2 and v3 dataset tag formats
 # Leave blank for latest versions

signalexe.py

@@ -229,7 +229,7 @@ def write_config_file(run_name, config_file, data_directory, opt_tasks):
 pangolin-data:
 
 # Versions for Nextclade (software & datasets)
-# nextclade: Software version. Input should use numbers only (i.e., 2.14.0)
+# nextclade: Software version. Input should use numbers only (i.e., 2.14.0). Must be >=1.3.0.
 # nextclade-data: The nextclade dataset tag. Refer to available nextclade datasets. Accepted tag format is 'YYYY-mm-ddTHH:MM:SSZ'
 # Be as specific as possible with the desired dataset tag. Can accept dates (YYYY-mm-dd) alone, but will assume corresponding timestamp (HH:MM:SS). SIGNAL will automatically adjust between v2 and v3 dataset tag formats
 # Leave blank for latest versions