Merge branch 'main' into new_schemes

bifrost_chewbbaca/datadump.py

@@ -28,7 +28,8 @@ def extract_cgmlst(cgmlst: Category, results: Dict, component_name: str) -> None
         lines = input.readlines()
         lines = [i.strip() for i in lines]
         locus_names = lines[0].split()[1:]
-        allele_values = lines[1].split()[1:]
+        allele_values = [int(x) if x.isdigit() else x for x in lines[1].split()[1:]]
+
         allele_dict = {
             locus_names[i]: allele_values[i] for i in range(len(locus_names))
         }

environment.yml

@@ -3,12 +3,14 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - snakemake-minimal>=5.31.1 # updated from 5.7.1 because of envvars
-  - blast>=2.14.0 # updated from blast>=2.9
-  - prodigal>=2.6.3
-  - chewbbaca>=3.2.0
+  - snakemake-minimal==5.7.1
+  - blast=2.9
+  - prodigal=2.6.3
+  - chewbbaca=3.2.0
   - pip
   - pip:
+    - jsonschema<4
+    - warlock==1.3.3
     - pytest
     - pytest-cov
     - pytest-profiling
@@ -17,5 +19,3 @@ dependencies:
     - argh
     - watchdog
     - bifrostlib
-    - black
-    - -e .

install.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+set -euo pipefail
+
 helpFunction()
 {
    echo ""
@@ -39,7 +41,7 @@ if [ "$parameterI" == "COMP" ]
 then
   echo "Starting computerome install"
   module load tools computerome_utils/2.0
-  module load tools anaconda3/2022.10
+  module load tools $CONDA_VERSION
   #if $BIFROST_CONDA_PATH is not set then exit with help message
   if [ -z "$BIFROST_CONDA_PATH" ]
   then
@@ -121,7 +123,7 @@ if test -f "$REQ_TXT";
 then
   echo "Making conda env"
   echo "$ENV_NAME will be created"
-  mamba env create -f "$REQ_TXT" --name $ENV_NAME
+  mamba env create --file "$REQ_TXT" --name $ENV_NAME
 else
   echo "environment.yml file cannot be found in the script folder"
   exit 1
@@ -148,7 +150,5 @@ fi
 if test -f "$CUSTOM_INSTALL_PATH";
 then
   echo -e "\nRunning custom_install.sh"
-  eval "$(conda shell.bash hook)"
-  conda activate $ENV_NAME
-  bash $CUSTOM_INSTALL_PATH -i $parameterI
-fi
+  bash -i $CUSTOM_INSTALL_PATH $ENV_NAME #-i required for interactive mode to active env
+fi