Fix for provenance

.github/workflows/main.yml

@@ -13,8 +13,8 @@ jobs:
       - uses: actions/checkout@v4
       - uses: ConorMacBride/install-package@v1
         with:
-          brew: bowtie2 bcftools bedtools
-          apt: bowtie2 bcftools bedtools
+          brew: bowtie2 bcftools bedtools fasttree
+          apt: bowtie2 bcftools bedtools fasttree
       - name: Install Python
         uses: actions/setup-python@v4
         # see details (matrix, python-version, python-version-file, etc.)

.github/workflows/publish_meteor.yml

@@ -25,7 +25,11 @@ jobs:
         with:
           context: .
           push: true
-          tags: ${{ secrets.DOCKER_USER }}/meteor:${{  github.ref_name }} , ${{ secrets.DOCKER_USER }}/meteor:latest
+          platforms: linux/amd64
+          provenance: false
+          tags: |
+            ${{ secrets.DOCKER_USER }}/meteor:${{  github.ref_name }}
+            ${{ secrets.DOCKER_USER }}/meteor:latest
 
   conda:
     runs-on: ubuntu-latest

README.md

@@ -14,12 +14,12 @@ Meteor relies on genes catalogue to perform species-level taxonomic profiling, f
 
 ## Dependencies
 
-Meteor requires:
+Besides python packages dependencies, Meteor requires:
 - python>=3.10
-- [bowtie2](https://github.com/BenLangmead/bowtie2)
-- [bcftools](https://samtools.github.io/bcftools/)
-- [FastTree](http://www.microbesonline.org/fasttree/)
-- [ete3](http://etetoolkit.org/)
+- [bowtie2 >=2.3.5](https://github.com/BenLangmead/bowtie2)
+- [bcftools >=0.1.19](https://samtools.github.io/bcftools/)
+- [bedtools >=2.18.0](https://bedtools.readthedocs.io/en/latest/index.html)
+- [FastTree >=1.9.0](http://www.microbesonline.org/fasttree/)
 
 ## Installation
 

meteor/variantcalling.py

@@ -274,10 +274,12 @@ def execute(self) -> None:
             sys.exit()
         start = perf_counter()
         with NamedTemporaryFile(
-            mode="wt", dir=self.meteor.tmp_dir, delete=False
+            mode="wt",
+            dir=self.meteor.tmp_dir,  # delete=False
         ) as temp_vcf_pileup:
             with NamedTemporaryFile(
-                mode="wt", dir=self.meteor.tmp_dir, delete=False
+                mode="wt",
+                dir=self.meteor.tmp_dir,  # delete=False
             ) as temp_vcf:
                 startpileup = perf_counter()
                 check_call(