From 54da840aa2e367bcb848ad87f030cf427faa031f Mon Sep 17 00:00:00 2001
From: Amine  GHOZLANE <amine.ghozlane@pasteur.fr>
Date: Tue, 5 Mar 2024 10:39:38 +0100
Subject: [PATCH] Fix meteor strain bug and condas build on github

---
 .github/workflows/publish_meteor.yml | 2 +-
 meteor/strain.py                     | 4 ++--
 meteor/variantcalling.py             | 5 ++++-
 3 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/publish_meteor.yml b/.github/workflows/publish_meteor.yml
index bd54ce8..cb31c48 100644
--- a/.github/workflows/publish_meteor.yml
+++ b/.github/workflows/publish_meteor.yml
@@ -32,7 +32,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: devtools/conda-envs/build_env.yaml
+          environment-file: conda/build_env.yaml
           auto-update-conda: false
           channels: conda-forge,bioconda,aghozlane,defaults
       - name: Build and upload the conda packages
diff --git a/meteor/strain.py b/meteor/strain.py
index ff26e1f..197209e 100644
--- a/meteor/strain.py
+++ b/meteor/strain.py
@@ -256,7 +256,7 @@ def execute(self) -> None:
             msp_file = (
                 self.meteor.ref_dir
                 / self.json_data["reference"]["reference_file"]["database_dir"]
-                / self.json_data["reference"]["annotation"]["msp"]
+                / self.json_data["reference"]["annotation"]["msp"]["filename"]
             )
             cram_file = (
                 self.json_data["mapped_sample_dir"]
@@ -265,7 +265,7 @@ def execute(self) -> None:
             bed_file = (
                 self.meteor.ref_dir
                 / self.json_data["reference"]["reference_file"]["database_dir"]
-                / self.json_data["reference"]["annotation"]["bed"]
+                / self.json_data["reference"]["annotation"]["bed"]["filename"]
             )
             start = perf_counter()
             # count_file,
diff --git a/meteor/variantcalling.py b/meteor/variantcalling.py
index c001c5a..ff69f56 100644
--- a/meteor/variantcalling.py
+++ b/meteor/variantcalling.py
@@ -212,10 +212,13 @@ def execute(self) -> None:
             / self.census["reference"]["reference_file"]["fasta_dir"]
             / self.census["reference"]["reference_file"]["fasta_filename"]
         )
+        print(self.meteor.ref_dir)
+        print(self.census["reference"]["reference_file"]["database_dir"])
+        print(self.census["reference"]["annotation"]["bed"])
         bed_file = (
             self.meteor.ref_dir
             / self.census["reference"]["reference_file"]["database_dir"]
-            / self.census["reference"]["annotation"]["bed"]
+            / self.census["reference"]["annotation"]["bed"]["filename"]
         )
         bcftools_exec = run(["bcftools", "--version"], capture_output=True)
         bcftools_version = (