removed standard_primer_agrep as it will probably need a container du…

…e to it needing the 'agrep' tool which doesn't exist in conda/pypi
EBI-Metagenomics · Jan 11, 2024 · 6368d91 · 6368d91
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commit 6368d91
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diff --git a/mgnify_pipelines_toolkit/analysis/amplicon/primer_agrep.sh b/mgnify_pipelines_toolkit/analysis/amplicon/primer_agrep.sh
diff --git a/mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_agrep.py b/mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_agrep.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -49,5 +49,4 @@ classify_var_regions = "mgnify_pipelines_toolkit.analysis.amplicon.classify_var_
 find_mcp_inflection_points = "mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main"
 make_asv_count_table = "mgnify_pipelines_toolkit.analysis.amplicon.make_asv_count_table:main"
 remove_ambiguous_reads = "mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main"
-rev_comp_se_primers = "mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main"
-standard_primer_agrep = "mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_agrep:main"
+rev_comp_se_primers = "mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main"
diff --git a/tests/unit/analysis/amplicon/standard_primer_agrep/test_standard_primer_agrep.yml b/tests/unit/analysis/amplicon/standard_primer_agrep/test_standard_primer_agrep.yml