feat: upgrade to use bgcflow wrapper v0.5.0 which use Snakemake v8.25.5

.github/workflows/build.yml

@@ -43,9 +43,9 @@ jobs:
       with:
         submodules: recursive
     - name: Set up Micromamba
-      uses: mamba-org/setup-micromamba@v1
+      uses: mamba-org/setup-micromamba@v2
       with:
-        micromamba-version: '1.5.8-0'
+        micromamba-version: '2.0.4-0'
         environment-file: ${{ matrix.environment }}
         init-shell: bash
         cache-environment: true

.github/workflows/push.yml

@@ -10,7 +10,7 @@ jobs:
       with:
         submodules: recursive
     - name: Formatting
-      uses: github/super-linter@v5
+      uses: github/super-linter@v6
       env:
         VALIDATE_ALL_CODEBASE: false
         DEFAULT_BRANCH: main
@@ -21,7 +21,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Linting
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/Snakefile
@@ -39,7 +39,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/Snakefile
@@ -57,7 +57,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/Report
@@ -75,7 +75,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/Metabase
@@ -93,7 +93,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/BGC
@@ -111,7 +111,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/ppanggolin
@@ -129,7 +129,7 @@ jobs:
       with:
         submodules: recursive
     - name: Dry-run workflow
-      uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c
+      uses: snakemake/snakemake-github-action@v1
       with:
         directory: .tests
         snakefile: workflow/lsabgc
@@ -145,7 +145,7 @@ jobs:
       - uses: actions/setup-python@v5
         with:
           python-version: 3.11
-      - run: pip install bgcflow_wrapper==0.4.0
+      - run: pip install "bgcflow_wrapper>=0.5.0"
       - run: pip install pytest-cov
       - run: pip install alive-progress
       - name: Test coverage

workflow/BGC

@@ -186,7 +186,7 @@ wildcard_constraints:
 rule all:
     input:
         expand("data/processed/{name}/tables/df_gtdb_meta.csv", name=PROJECT_IDS),
-        get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules_bgc.yaml"),
+        get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules_bgc.yaml"),
 
 # Create place holder for resources defined in each modules, will be added if module is included, and passed to create custom_resource_dir
 resource_mapping = {}

workflow/Database

@@ -10,7 +10,7 @@ version = dependency_version["antismash"]
 
 ##### Make sure all required inputs exist
 NCBI = DF_SAMPLES[DF_SAMPLES.source.eq("ncbi")].genome_id.to_list()
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules.yaml", ignore_missing=True)
 
 error_message = " * Has the jobs from the main workflow finished?\n * Check by running: 'bgcflow run -n'"
 for main_pipeline_outputs in final_outputs:

workflow/Snakefile

@@ -49,7 +49,7 @@ wildcard_constraints:
 
 ##### Target rules #####
 
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules.yaml", ignore_missing=True)
 
 rule all:
     input:

workflow/envs/alleleome.yaml

@@ -2,7 +2,6 @@ name: alleleome
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python==3.11
   - mafft==7.505

workflow/envs/amrfinderplus.yaml

@@ -2,6 +2,5 @@ name: amrfinder
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   -  ncbi-amrfinderplus

workflow/envs/antismash.yaml

@@ -2,7 +2,6 @@ name: antismash_env
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - meme=4.11.2
   - python>=3.9

workflow/envs/antismash_v6.yaml

@@ -2,7 +2,6 @@ name: antismash_6
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - meme==4.11.2
   - python>=3.9

workflow/envs/arts.yaml

@@ -1,7 +1,6 @@
 name: arts_env
 channels:
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
   - python==3.8

workflow/envs/automlst_wrapper.yaml

@@ -2,7 +2,6 @@ name: automlst_wrapper
 channels:
   - bioconda
   - conda-forge
-  - anaconda
 dependencies:
   - python=2.7
   - Flask=0.12.2

workflow/envs/bgc_analytics.yaml

@@ -2,9 +2,8 @@ name: bgc_analytics
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - python>=3.9,<3.10
+  - python==3.11
   - jupyterlab>3
   - ipywidgets>=7.6
   - jupyter-dash
@@ -16,11 +15,11 @@ dependencies:
   - python-kaleido
   - bokeh
   - openpyxl
-  - nbconvert==6.4.2
+  - nbconvert
   - ipykernel
   - ete3
   - pyarrow
-  - peppy==0.35.7
+  - peppy
   - xlrd >= 1.0.0
   - zip
   - altair
@@ -34,4 +33,4 @@ dependencies:
       - networkx
       - alive_progress
       - python-louvain
-      - ncbi-genome-download==0.3.3
+      - ncbi-genome-download

workflow/envs/bgcflow_notes.yaml

@@ -2,7 +2,6 @@ name: bgcflow_notes
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python>=3.9,<3.12
   - jupyterlab>3

workflow/envs/cblaster.yaml

@@ -1,7 +1,6 @@
 name: cblaster
 channels:
   - conda-forge
-  - default
   - bioconda
 dependencies:
   - diamond==2.1.9

workflow/envs/checkm.yaml

@@ -2,7 +2,6 @@ name: checkm
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python==3.11
   - numpy==1.26.4

workflow/envs/clinker.yaml

@@ -2,7 +2,6 @@ name: clinker
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - pip
   - pip:

workflow/envs/convert_genbank.yaml

@@ -2,7 +2,6 @@ name: convert_gbk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - any2fasta==0.4.2
   - biopython>=1.80

workflow/envs/dbt-duckdb.yaml

@@ -2,7 +2,6 @@ name: dbt-duckdb
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - python==3.11
   - python-duckdb==1.0.0

workflow/envs/deeptfactor.yaml

@@ -2,7 +2,6 @@ name: deeptfactor
 channels:
   - pytorch
   - gurobi
-  - defaults
   - conda-forge
   - bioconda
 dependencies:

workflow/envs/fastani.yaml

@@ -2,7 +2,6 @@ name: fastani
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - fastani=1.33
   - gsl=2.7=he838d99_0

workflow/envs/gecco.yaml

@@ -1,7 +1,6 @@
 name: gecco
 channels:
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
   - gecco=0.9.10

workflow/envs/getphylo.yaml

@@ -1,7 +1,6 @@
 name: getphylo
 channels:
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
   - diamond

workflow/envs/gtdbtk.yaml

@@ -2,7 +2,6 @@ name: gtdbtk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - gtdbtk=2.4.0
   - wget

workflow/envs/lsabgc.yaml

@@ -1,6 +1,5 @@
 name: lsaBGC
 channels:
-  - defaults
   - bioconda
   - conda-forge
 dependencies:

workflow/envs/mash.yaml

@@ -2,7 +2,6 @@ name: mash
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - mash=2.3
   - gsl=2.6

workflow/envs/mlst.yaml

@@ -2,6 +2,5 @@ name: mlst
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - mlst=2.19.0

workflow/envs/mmseqs2.yaml

@@ -2,7 +2,6 @@ name: mmseqs2
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - mmseqs2
   - any2fasta

workflow/envs/ppanggolin.yaml

@@ -3,6 +3,5 @@ channels:
   - conda-forge
   - bioconda
   - r
-  - defaults
 dependencies:
   - ppanggolin=1.2.105

workflow/envs/prokka.yaml

@@ -2,6 +2,5 @@ name: prokka_env
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - prokka=1.14.6

workflow/envs/r_notebook_bgc.yaml

@@ -2,7 +2,6 @@ name: r_notebook_bgc
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - r-base==4.1.3
   - jupyterlab>3

workflow/envs/refseq_masher.yaml

@@ -2,6 +2,5 @@ name: refseq_masher
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - refseq_masher=0.1.2

workflow/envs/roary.yaml

@@ -2,7 +2,6 @@ name: roary_env
 channels:
   - bioconda
   - conda-forge
-  - defaults
 dependencies:
   - python<3.12
   - roary=3.13.0

workflow/envs/seqfu.yaml

@@ -2,6 +2,5 @@ name: seqfu
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - seqfu=1.20.3

workflow/envs/utilities.yaml

@@ -1,7 +1,6 @@
 name: utilities
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - openjdk
   - perl

workflow/ppanggolin

@@ -51,7 +51,7 @@ wildcard_constraints:
 
 ##### Target rules #####
 
-final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="workflow/rules_ppanggolin.yaml", ignore_missing=True)
+final_outputs = get_final_output(DF_SAMPLES, PEP_PROJECTS, rule_dict_path="rules_ppanggolin.yaml", ignore_missing=True)
 
 rule all:
     input:

workflow/rules/common.smk

@@ -8,8 +8,8 @@ from snakemake.utils import min_version
 from pathlib import Path
 import peppy
 
-min_version("7.14.0")
-__version__ = "1.1.2"
+min_version("8.25.5")
+__version__ = "1.2.0"
 
 
 container: "docker://matinnu/bgcflow:latest"
@@ -728,7 +728,7 @@ def get_project_outputs(
     Returns:
         final_output {list} -- list of final output files
     """
-    with open(workflow.source_path(f"../../{rule_dict_path}"), "r") as file:
+    with open(workflow.source_path(rule_dict_path), "r") as file:
         rule_dict = yaml.safe_load(file)
 
     selection = [