mgnify-pipelines-toolkit 1.2.9__py3-none-any.whl → 1.2.11__py3-none-any.whl

mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py

@@ -167,7 +167,8 @@ def main():
             matched_primers_list.append(cleaned_primer_name)
 
     res_df = pd.DataFrame.from_dict(res_dict)
-    res_df.to_csv(f"./{sample}_primer_validation.tsv", sep="\t", index=False)
+    res_tsv_name = f"./{sample}_primer_validation.tsv"
+    res_df.to_csv(res_tsv_name, sep="\t", index=False) if not res_df.empty else open(res_tsv_name, "w").close()
 
     fwd_primers_fw.close()
     rev_primers_fw.close()

mgnify_pipelines_toolkit/schemas/schemas.py

@@ -72,12 +72,13 @@ class INSDCRunAccession(RootModel):
 
 
 class AmpliconResultTypes(StrEnum):
-    """Class that models the two allowed statuses for successful amplicon analysis runs.
+    """Class that models the three allowed statuses for successful amplicon analysis runs.
     Pydantic validates Enums very simply without needing to declare a new function.
     """
 
     all_results = "all_results"
     no_asvs = "no_asvs"
+    dada2_stats_fail = "dada2_stats_fail"
 
 
 class AmpliconPassedRunsRecord(BaseModel):

{mgnify_pipelines_toolkit-1.2.9.dist-info → mgnify_pipelines_toolkit-1.2.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.2.9
+Version: 1.2.11
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0

{mgnify_pipelines_toolkit-1.2.9.dist-info → mgnify_pipelines_toolkit-1.2.11.dist-info}/RECORD

@@ -4,7 +4,7 @@ mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=8yFhmH
 mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=-g1FDwdEndWH9VvYLmc_NEs2l204kKjMHk65wag8T_s,8891
 mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py,sha256=BLqhflblUegCvuQic16PrFXfIXlFWmGkmWJyl4wJoLQ,5040
 mgnify_pipelines_toolkit/analysis/amplicon/permute_primers.py,sha256=1aGOJX9tC7M1rnd0U2PeJ681sUo02wxk7_ycJqeVt6s,2216
-mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=-W_QmdmKAIqVC5n-RS8LX11hEQM4xdp5r1jkITB1CI8,5256
+mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=uGlQ0595rammsW-rnhh1UAEkoRUjLqCQ-tp377Mj180,5345
 mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=Wu4tRtuRkgd3hoeuwPl_E5ghxIW7e_1vrcvFGWv_U4A,3173
 mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py,sha256=yLpzkRJXAeXRUNgz60zopEwHcdprM2UDjquE-GkrFys,1722
 mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py,sha256=epVClL10QcllL8yu7YGjx0rXNVHL2GxHi-Ek0MOjsjo,13859
@@ -40,13 +40,13 @@ mgnify_pipelines_toolkit/constants/regex_fasta_header.py,sha256=G-xrc9b8zdmPTaOI
 mgnify_pipelines_toolkit/constants/tax_ranks.py,sha256=ekZN5OcMBhDRcj7XB_27wQ8fEnmAqMJc4aQ3pv4BRmI,1229
 mgnify_pipelines_toolkit/constants/thresholds.py,sha256=1AMBmoHBR0WjXZpkwJ7_Q-gfJtHXuCA4tZ-uvPhF0Xc,1085
 mgnify_pipelines_toolkit/constants/var_region_coordinates.py,sha256=0bM4MwarFiM5yTcp5AbAmQ0o-q-gWy7kknir9zJ9R0A,1312
-mgnify_pipelines_toolkit/schemas/schemas.py,sha256=he9igC80YTR32v1e5NslwTgtdVySmnXwK9iY9IBPNBg,23133
+mgnify_pipelines_toolkit/schemas/schemas.py,sha256=0l1hOkF4AeN0YOm4CVGPoP-U8kEzAxbhNEk3VEezZ4g,23177
 mgnify_pipelines_toolkit/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mgnify_pipelines_toolkit/utils/fasta_to_delimited.py,sha256=lgYIR1S4crURY7C7nFtgE6QMV4u4zCNsUrVkcRnsEEo,3996
 mgnify_pipelines_toolkit/utils/get_mpt_version.py,sha256=aS9bWrC9CP7tpxoEVg6eEYt18-pmjG7fJl5Mchz4YOU,798
-mgnify_pipelines_toolkit-1.2.9.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mgnify_pipelines_toolkit-1.2.9.dist-info/METADATA,sha256=hxvefbAKXzSx05LR0jTdW3iW2fHlr2hxmNhY4TCdJ_4,5775
-mgnify_pipelines_toolkit-1.2.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-mgnify_pipelines_toolkit-1.2.9.dist-info/entry_points.txt,sha256=7TJ8GgbKoX1xnQsOdWwMvwhIv4uuHCx7pMxKmZabPOs,3228
-mgnify_pipelines_toolkit-1.2.9.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
-mgnify_pipelines_toolkit-1.2.9.dist-info/RECORD,,
+mgnify_pipelines_toolkit-1.2.11.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mgnify_pipelines_toolkit-1.2.11.dist-info/METADATA,sha256=xziE8NaQ8tsUlY9JTEOX4Sf5KO4xnzD2hRL-nvHFryw,5776
+mgnify_pipelines_toolkit-1.2.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+mgnify_pipelines_toolkit-1.2.11.dist-info/entry_points.txt,sha256=7TJ8GgbKoX1xnQsOdWwMvwhIv4uuHCx7pMxKmZabPOs,3228
+mgnify_pipelines_toolkit-1.2.11.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
+mgnify_pipelines_toolkit-1.2.11.dist-info/RECORD,,