Fix(pipeline): prevent nested zip packaging and update CRISPR dependencies

- Add filter to skip .zip and .tar.gz files when creating result archive
- Update CRISPR feature with CASFinder dependencies (hmmer, blast, vmatch, etc.)
- Add install-casfinder task for macsydata installation
- Remove obsolete CRISPR test files

Co-Authored-By: Claude <noreply@anthropic.com>

pixi.toml

@@ -63,12 +63,27 @@ pytest = "*"
 #
 # 预期依赖（待激活时添加）:
 [feature.crispr.dependencies]
-python = ">=3.9"
-# crisprcasfinder = "*"  # 需要配置安装源
-biopython = "*"
-pandas = ">=2.0.0"
+python = ">=3.10"
+wget = "*"
+curl = "*"
+git = "*"
+java-jdk = "*"
+parallel = "*"
+perl-app-cpanminus = "*"
+hmmer = "*"
+emboss = "*"
+blast = "*"
+perl-bioperl-core = "*"
+perl-xml-simple = "*"
+perl-digest-md5 = "*"
+vmatch = "*"
+muscle = "*"
+prodigal = "*"
+mamba = "*"
+macsyfinder = "==2.1.2"
 
 [feature.crispr.tasks]
+install-casfinder = "macsydata install -u CASFinder==3.1.0"
 detect = "python tools/crispr_cas_analysis/scripts/detect_crispr.py"
 fusion = "python tools/crispr_cas_analysis/scripts/fusion_analysis.py"
 
@@ -80,7 +95,7 @@ digger = ["digger"]
 pipeline = ["pipeline"]
 frontend = ["frontend"]
 webbackend = ["webbackend"]
-crispr = ["crispr", "pipeline"] # Inherit pipeline to get pandas etc? Or just pipeline deps. Let's make crispr feature add to pipeline env if possible, or just use pipeline env for running these tools since they are python.
+crispr = ["crispr"]
 
 # Actually, let's keep it simple. The tools are Python scripts. They can run in the 'pipeline' environment which has python and pandas.
 # The 'crispr' feature defines dependencies.