fix(ci): update black to rev 22.3.0

.github/workflows/main.yml

@@ -133,6 +133,7 @@ jobs:
       - name: Test rule ${{ matrix.rule }} on ${{ matrix.technology }} ${{ matrix.seq_method }} data
         uses: snakemake/[email protected]
         with:
+          stagein: mamba env create -f workflow/envs/trinity.yaml -n trinity
           directory: .tests
           snakefile: workflow/Snakefile
           args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}"

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
       - id: snakefmt
 
   - repo: https://github.com/psf/black
-    rev: 21.12b0
+    rev: 22.3.0
     hooks:
       - id: black
       - id: black-jupyter

workflow/envs/trinity.yaml

@@ -1,5 +1,8 @@
 channels:
   - bioconda
   - conda-forge
+  - defaults
 dependencies:
-  - trinity =2.12
+  - trinity =2.13
+  # ensure that we use a bowtie2 that already contains fixed dependency constraints
+  - bowtie2 =2.4.5

workflow/rules/benchmarking.smk

@@ -241,7 +241,7 @@ rule assembly_comparison_trinity:
         "../envs/trinity.yaml"
     shell:
         "(Trinity --left {input.fastq1} --max_memory 16G --right {input.fastq2} --CPU {threads} --seqType fq --output {params.outdir} && "
-        "mv {params.outdir}/Trinity.fasta {output} ) > {log} 2>&1"
+        "mv {params.outdir}.Trinity.fasta {output} ) > {log} 2>&1"
 
 
 rule assembly_comparison_velvet:

workflow/scripts/evaluate-strain-call-error.py

@@ -45,9 +45,7 @@ def load_pangolin_df(i, path):
         columns={"lineage": "target_id", "scorpio_support": "est_fraction"},
         inplace=True,
     )
-    pangolin_df.drop(
-        columns=["taxon", "pangoLEARN_version", "qc_status", "note"], inplace=True
-    )
+    pangolin_df.drop(columns=["taxon", "qc_status", "note"], inplace=True)
     pangolin_df["mix"] = i
     return pangolin_df