abi/__init__.py,sha256=FnwF-iDWgW3YeYD4w3Gt0_8sRcsWyARvz5GpaG5YRWg,5454
abi/_shared.py,sha256=spb5-gKa2iUEjs_2jnbDGB3ak5MXrRWmDRItFG_UlO4,13948
abi/cli.py,sha256=-frZpP0ZzX8zbXAot6Emzp43gJ180Oq6f3hKs4o5smM,89341
abi/config.py,sha256=ZJ6sfXHZWuZwREPcEH4rxGObKO7KPEtvJjdthoojaTc,4409
abi/dag.py,sha256=THOlOPtCb24Q3LA-A9UajEOTZ-nQk3y_nHdGZET00Qw,11980
abi/diagnostics.py,sha256=6GOLSwyTPIqCuFJiqrQAfc-P_m5nWTSuTN3dyiXr0ns,17822
abi/errors.py,sha256=vAu1UbPP6EeG6w8n8Yt34Wkxb8-ucgpglJynR5n_En8,6476
abi/executor.py,sha256=2NpYCyq2VYS9PdiLxDiu03irdxVyiItT6GHwp-cCnFg,53333
abi/filesystem.py,sha256=Cp-mP2ZChqoMAIJ6ikIJibldkjqpKhll8NZuNfoSAvc,585
abi/interfaces.py,sha256=NWKUVdXppQ5BCpHMkh2HS3ngOOpi_oyv6f6YRKJrHPU,14238
abi/json_utils.py,sha256=sX34ZdjWPAII3ZSvX22D_IduQ7kbY8-cIE9J16Ku7iw,1634
abi/openai_contracts.py,sha256=tKBJmUFRfoENmHb9pMlk1e1gVStPO9VGFNp5WDp69kU,826
abi/permissions.py,sha256=4mhgs9QhHNxAFple02qH58Jit4TNlIzmWy0RE0op9rY,7829
abi/provenance.py,sha256=OnYo7cPqWhCs7Jh_Bpi1wGhhJNN4GRKjnpRBwWJzZQU,37723
abi/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
abi/resources.py,sha256=jV47HRM8SORVeGNtuiSMkd_J_qowHPhFdOIdNdlZOq8,17022
abi/results.py,sha256=uxLrQxB-5OzgktPhUV5vwCgcKycyA-Y1TkKR9UoUwDU,13529
abi/schemas.py,sha256=4yw_TYWcIwcuqqfePVYg4Yc3t78rNtELj5rBN6LsqbU,24095
abi/tables.py,sha256=dKqjbrGjZgCifBPuk1xWZC-o9DMqQRPDtMPEzPYLncc,9691
abi/testing.py,sha256=3pLX5R60VQeyoT94-AESQN8sK_SIba5f-c9Mwlq0t9I,1957
abi/timeouts.py,sha256=fYbAR6nNnZZVoggnknk2Edi3wqhOixAApEG-w4DXnws,1429
abi/tool_descriptors.py,sha256=_U2DNcuwn7E6FmrJBHU93OcFdca7f2FUx9gdIKKuM-U,26908
abi/tools.py,sha256=uX_yHF1tMYMzTnRdP1zWwsIQDxqyXGjCz4NUHGw7AsU,74608
abi/agent/__init__.py,sha256=cP-LG432PGvS7tykHoQ2knJjN0SxBnNZGDLlSLr6qXc,115
abi/agent/context.py,sha256=Z9UwacBkmT_IGpRcCIXN_BdFTFGKDpi__jSiNip4tbA,8320
abi/agent/envelopes.py,sha256=H9duq3m5ChTNFhR2p8asSYM42AxLVwVx7zG_VopFSTY,7768
abi/agent/interface.py,sha256=3qKE3iGuK-gP6grKrCVHHaVCWUPECmuGwyOL8WNVKy8,51653
abi/autoplasm/__init__.py,sha256=Dy3LT7EhwOVkrjJIS7YGrEghOOs9gvKguQKXoxQh4D8,147
abi/autoplasm/cli.py,sha256=gWWu2fMyQozjXJ1k_LJ_xIgsPV8741wpHIISJzEDkoI,571
abi/autoplasm/config.py,sha256=jiKjgB-1BZ9X4PvLEL__c9ovSS4N3GpYL_butw9CXT0,580
abi/autoplasm/dashboard.py,sha256=iKJDszROuJDXSWQeZ3ULdfd-3cdsqDhvPNtDgWOws2U,589
abi/autoplasm/filesystem.py,sha256=IrARXNEQjT_1WuUM9GyjNMh27xjzsqzgl_5zpaDQGsw,592
abi/autoplasm/json_utils.py,sha256=PuZ1M1y1U6CJZop49pwP-EywdoEMpXxjZ62uYvo63pc,592
abi/autoplasm/logger.py,sha256=UQNZVg9hh8eC6lijpsprQXiyktIFMSJjtbSk7iJpr_4,580
abi/autoplasm/parsers.py,sha256=6FyWr-Ga-zhAxb36EwjW99GCrUbc3ctMpx2UiHHsEdA,583
abi/autoplasm/pipeline.py,sha256=xL70Ug8t_odazZPUfI1p5YJU9jFksEmZlg_1AvW_uTk,586
abi/autoplasm/planner.py,sha256=XZXX8lq8FSi6KnED_Ah8NrjT9C2xfwxHEquTJm-jHko,583
abi/autoplasm/progress.py,sha256=zpeVngghyG7LVe1jZjA5NOzfA5g_fJ52MdJJV0MA7NI,586
abi/autoplasm/resources.py,sha256=dEVkFj6J-agt8K05YODH5NkPf6RGH8W_F6ENPNe-etM,589
abi/autoplasm/result_validation.py,sha256=YCvosygBA5i-FBDVaciX1Vl5DlEGmh236bGX9TczBxg,540
abi/autoplasm/sample_sheet.py,sha256=YUWfQeFJBjFiNXYbHRbSWHgUGA54F8hciSxPX7ymU5Y,598
abi/autoplasm/schemas.py,sha256=PSga4Fk0Wy7OZxgG2d198MkdpmPejNeZghcm-py8K_0,583
abi/autoplasm/selectors.py,sha256=q9x6kruIPeA6xKZ7DHEYx0HwNN3vBttdNm75oVkwlrs,589
abi/autoplasm/standard_tables.py,sha256=gd18Iwy-iFwXEqdsGT0frJO_5JQ3j4HcL9gVqOEEqX4,536
abi/autoplasm/statistics.py,sha256=x8uA9MhYQdK1VXshYkArrmAra5eIqY8zcBmW3pL-gyw,592
abi/autoplasm/timeouts.py,sha256=1V5NLhT3EgoPBd528ZwAQffXTt-nJzgrpVpMiamYssQ,586
abi/autoplasm/normalize/__init__.py,sha256=2rjXDmVpSNIM4zBuPOKjdxA1JcaZfp76FxwBOCowfL8,35
abi/autoplasm/normalize/abundance.py,sha256=1-v1RrGIUKSa6LDEwoBXW-fuJoF8Rd29eZiYTVot1ik,594
abi/autoplasm/normalize/annotation.py,sha256=Tnf2c8txv3ChF831AIvN3PbMuyEud7upaxjSa62vlbk,515
abi/autoplasm/normalize/plasmid_prediction.py,sha256=zOELdCV6gZxapsp0cuHjRLens-ZOeXZ_KE3tb_Y0T3c,531
abi/autoplasm/report/__init__.py,sha256=2rjXDmVpSNIM4zBuPOKjdxA1JcaZfp76FxwBOCowfL8,35
abi/autoplasm/report/html.py,sha256=gIYg3JBICQ23xGXT-niFcOK2jSdVgyVKVqsu50LAfAU,564
abi/autoplasm/report/markdown.py,sha256=4Gm21Vfu4_DR36CCOMpyo_NCHlxpXy_iCIbW1l472_M,505
abi/autoplasm/skills/__init__.py,sha256=2rjXDmVpSNIM4zBuPOKjdxA1JcaZfp76FxwBOCowfL8,35
abi/autoplasm/skills/abundance.py,sha256=h0FEnm_i4lsbAldRDIVvXi-7LOggCGo-ftPysE-98Tc,507
abi/autoplasm/skills/annotation.py,sha256=KxmNQymi5Q8qaWrrADDSlXlvzuTPv2TGvBz45_vOk1E,509
abi/autoplasm/skills/assembly.py,sha256=sY_PQ70fGJM1Xv5WD0yYv8NOQkTA3g8fv_Efpvr7MsI,505
abi/autoplasm/skills/base.py,sha256=1Yq-Yoz4tNMROj5lPpHFnGPaPDmdlLV2-3vyoQgdua0,564
abi/autoplasm/skills/host_prediction.py,sha256=p5sbzbGiDZM8bjWRV5oXEs7-uVMVSpCv35bJusWMJfs,519
abi/autoplasm/skills/plasmid_binning.py,sha256=EyhByDD5OsqyWgfYs_pXhtD2VZAzHOoPlnHCxAot_8c,519
abi/autoplasm/skills/plasmid_detection.py,sha256=I_M-ZJACLIdhcTbBqbaoPLK6CDCQ5xnDKo-xaAYkMqI,523
abi/autoplasm/skills/qc.py,sha256=27jaUdPibeAuUUCwV5ZbdPoLUfRc0m9PgDIcbV6wfss,558
abi/autoplasm/skills/registry.py,sha256=_ldp3HmAkF3WJ3coghKhm49rTMwSJAzPd7GRYM-eTnc,505
abi/autoplasm/skills/statistics.py,sha256=X-7zd0KdVzXSOyoxzMW4hwokSez3lIY4z7qCktWDXuI,509
abi/autoplasm/skills/typing.py,sha256=TmC9T4B70fZZaM6Iq3CusiycCLp9kmJf9UD3euVv1Qo,501
abi/autoplasm/skills/visualization.py,sha256=luMu-fs9_UE2KoR8IGa770AJ31E2tQjngRfL9Zmsilk,515
abi/contracts/__init__.py,sha256=IU5vr3DWG4KtA4vzHZfYTPt6bHPUF5TE3Qt9N-R6bSs,19213
abi/contracts/lint.py,sha256=oQjXrLXdvwpBWYIeHz2FMyFwP2KJ1QCgMM-FJSF2SCU,19382
abi/contracts/step_contract.py,sha256=zz2PqW-oo0v8izKAS_YUvNbBGM9OlNvbnDH544FaAtU,36772
abi/exporters/__init__.py,sha256=vYX7nI6qSNOlhbmpuS-mD3og9-exdhBvTcRTWVJgc1c,111
abi/exporters/nextflow.py,sha256=bY_CuPRiPNcR23Nkexhz4BS0ByJ4vrD1PUQLqhGnK_E,16092
abi/figures/__init__.py,sha256=Q6y8bVRIF9kYJSNX0ET2CCTwxSnxEEFVzUP09u3TlYQ,834
abi/figures/base.py,sha256=FjhbBBSkDX8So38gIUe4vZlMRPlcXAU6Z2ooz9q7H-k,20747
abi/jobs/__init__.py,sha256=QfepUh9nmw6edwuNdCWxBNtnEnWBBMScgLwM8kU2WgE,323
abi/jobs/client.py,sha256=ScjIrr5Y4J1lJ_jVZCt9J4SmiHmgeZqZh58ITGwtuFM,2870
abi/jobs/service.py,sha256=EpX-dmH1UrGH1qKvAQ6wbVNQWurUJFqksc3e2cXKhPg,62237
abi/mcp/__init__.py,sha256=2EpD6Wuysyi9GmTdz9Nh1K8FhkTyR8xmV1MKNP6LFyI,50
abi/mcp/server.py,sha256=bp9yXW2Y5vp5sif4cav-ygmPPHB8CqTXfeii-rk_gL4,4566
abi/plugins/__init__.py,sha256=woU_rieKBuuQwx_HbZEAvG0vRorobSBchWGazNpVnok,2343
abi/plugins/amplicon_16s.py,sha256=G5XViTkAR4UpOyes2ipOR3Yg1YBwcRTPzJgvbfGolOo,31416
abi/plugins/metatranscriptomics.py,sha256=_tCh2baPPuLiUO-b94VXq64C5ED1UkZoYm6QpPu5Ad0,25476
abi/plugins/rnaseq_expression.py,sha256=rGpwvRsmcb9xtXTzbRL7KbPpRz51z9lWVDSrNofnudM,22770
abi/plugins/wgs_bacteria.py,sha256=d-Xgyh62AQXFhzVXeWKPpKsMeh-UI-s6Ze0SfqMRMbI,19289
abi/plugins/metagenomic_plasmid/__init__.py,sha256=4GXA78_P7Z406-jZA0RZh8Vx-tKz2Xa5FTxfAcj2GNA,14419
abi/plugins/metagenomic_plasmid/_engine/__init__.py,sha256=Dy3LT7EhwOVkrjJIS7YGrEghOOs9gvKguQKXoxQh4D8,147
abi/plugins/metagenomic_plasmid/_engine/cli.py,sha256=XtrALCr8QMHazbjniN9PQBzL4VSRiKCQfMxa5WAjsdo,41828
abi/plugins/metagenomic_plasmid/_engine/config.py,sha256=YRkyTabof5KOwL9sGPLEH6nNvLw3xeZ-Byqh1hmeSMs,8873
abi/plugins/metagenomic_plasmid/_engine/dashboard.py,sha256=k-KipMpW-SPfO4TOISXNyd5NquFmttIOoxLqj6m5pF0,17253
abi/plugins/metagenomic_plasmid/_engine/filesystem.py,sha256=pEThMKlzP6nRndK-MbWD3dZVSMy1YtCalFNaAjXN8kA,609
abi/plugins/metagenomic_plasmid/_engine/json_utils.py,sha256=GMrwWQuORwapeXzuVtnzlpmkxDagPcWGUmdLp_40fqA,1565
abi/plugins/metagenomic_plasmid/_engine/logger.py,sha256=u5Zfn-Hg9YiTUXW322EXRbrdl7YyTAPFBDONSuViWWI,3715
abi/plugins/metagenomic_plasmid/_engine/parsers.py,sha256=DYN8uhRmozWOsem8YWqFPvPj0AI7RQ9MH5YElGa--MI,46504
abi/plugins/metagenomic_plasmid/_engine/pipeline.py,sha256=SDSu81fxMil_b-j9Rh9y2ckSo7hk19wjE6CMiUnkom0,33805
abi/plugins/metagenomic_plasmid/_engine/pipeline_dag.py,sha256=m4GSvef7KUV5muu1jrdlhNMR-0RwWNY98d9Fjqa3Bv0,13174
abi/plugins/metagenomic_plasmid/_engine/planner.py,sha256=nvYU9ahujQqc1qZ7w1kYt0Tmi4mfhm-J-6UpuPq0gEA,35708
abi/plugins/metagenomic_plasmid/_engine/progress.py,sha256=HMoJ_o0gBgDO1HkOKMihp2T-W5wQQqpBTnxufpb_ZtQ,13016
abi/plugins/metagenomic_plasmid/_engine/resources.py,sha256=vabd-gZq9W2SGJrLp-TEN-tFU8_5Ygk6nAcVl5rDXz4,26124
abi/plugins/metagenomic_plasmid/_engine/result_validation.py,sha256=o9egXIPwTfSAfRJ34i0BriMtV8HQM374OecSQfeSxtY,4228
abi/plugins/metagenomic_plasmid/_engine/sample_sheet.py,sha256=vSDvAyzqTDOhy1nPvI_zXSaRrmNyANWm09Qg0dNzIeA,7305
abi/plugins/metagenomic_plasmid/_engine/schemas.py,sha256=4EOpY8KS0T4R-8GfRVR6usV66qAvZHvHpwsF5C4eOWk,691
abi/plugins/metagenomic_plasmid/_engine/selectors.py,sha256=0o-msx_5YW3H24GIu_EDXOrwt1atpOV0uAHEJHiY20U,846
abi/plugins/metagenomic_plasmid/_engine/standard_tables.py,sha256=Yq8rE2eISQFwJycz0cHAX3hLWeqqE4ORhfGA8vgs5ms,13172
abi/plugins/metagenomic_plasmid/_engine/statistics.py,sha256=xW5O6onC2LFxZxavZY5tHmBDRAbOVRHAjVvuE3yzooc,12622
abi/plugins/metagenomic_plasmid/_engine/timeouts.py,sha256=AgoRp9r3-JHFeXfN5XTTmQt-scZH1cRt2-4vKk24WnQ,1425
abi/plugins/metagenomic_plasmid/_engine/normalize/__init__.py,sha256=Cy_5xVE892eakEbSAfTPNuYiG9Yc5Oz_AnYCFMsHtaE,36
abi/plugins/metagenomic_plasmid/_engine/normalize/abundance.py,sha256=ZeWinsWJ8_ba8wwb06VbEG0sDOul_BcAaImlJTDGhoI,891
abi/plugins/metagenomic_plasmid/_engine/normalize/annotation.py,sha256=dnCocRUJzClBhNgZy0hk3-udOCKL_HIV_N6dsBsNQS0,863
abi/plugins/metagenomic_plasmid/_engine/normalize/plasmid_prediction.py,sha256=M4KnPfagpVHvXltvn_ff3eMD-kb5A-9zUTsbx0Wg-M4,2922
abi/plugins/metagenomic_plasmid/_engine/report/__init__.py,sha256=yv46q1xYNiaFqZISjnN8g4hST1bBGqX_PRd7sgAU0Eg,33
abi/plugins/metagenomic_plasmid/_engine/report/html.py,sha256=84aPahjcW-30zJazur5xFXrt8LnTrOa4ej6ZV53YUos,11251
abi/plugins/metagenomic_plasmid/_engine/report/markdown.py,sha256=w90Q4xK03YAwPeITnbkMin-IAwZSwUfw8gomFtX2COM,13223
abi/plugins/metagenomic_plasmid/_engine/skills/__init__.py,sha256=3DUU6Kn5ppW32hxsImm4E89vUY0ej0-TlSueqRkUlHI,37
abi/plugins/metagenomic_plasmid/_engine/skills/abundance.py,sha256=YHyHUWzQ_986m3BkOa_blW2PUKNVBdpTUi7KdRRH0qc,256
abi/plugins/metagenomic_plasmid/_engine/skills/annotation.py,sha256=sK6_bvQsD5IdfsZdgDcuAyHPDZx8k1d7zykP6SuF87g,257
abi/plugins/metagenomic_plasmid/_engine/skills/assembly.py,sha256=MZNLuCrWPFRElwuMa9GW_oa9gdSjpr_CemJ6TKt6tgE,260
abi/plugins/metagenomic_plasmid/_engine/skills/base.py,sha256=3OCPxXfH_s9NDOCWsVemCs7gjVmC0h7OzDFKkXGEGgI,13891
abi/plugins/metagenomic_plasmid/_engine/skills/host_prediction.py,sha256=sMklvg2IaYvr7Q_f888acKLMbkX32jHZd5s3d1cLhtg,262
abi/plugins/metagenomic_plasmid/_engine/skills/plasmid_binning.py,sha256=SUF3ZapKumdTvw-A5nKncEgdJCprINpkf2a3f5kge_Y,262
abi/plugins/metagenomic_plasmid/_engine/skills/plasmid_detection.py,sha256=nLh4t-BN5ES91K1PBLe-oYk3yABEH03xdP0_S5Qo07o,264
abi/plugins/metagenomic_plasmid/_engine/skills/qc.py,sha256=JWjOLlCGl-TR4CoNkmL9AjHGQzkuw7EQSD5jKbvBXvA,254
abi/plugins/metagenomic_plasmid/_engine/skills/registry.py,sha256=mGVmPK8UT3alhWPm6NS20gjeVInwm_QxDPPVO4wLcI4,5516
abi/plugins/metagenomic_plasmid/_engine/skills/statistics.py,sha256=9PcfykBtHigFIb0YmvlLP1NNYOjA-iV28mxpycBC4D4,257
abi/plugins/metagenomic_plasmid/_engine/skills/typing.py,sha256=RxliZj0vx2oan6PHx5UNRbckb8KctJUUZ9Y5nA-1kzE,261
abi/plugins/metagenomic_plasmid/_engine/skills/visualization.py,sha256=LtTvApXGtS3o7u9N7l-LA7UNgK1mkI3xwUTd00MD_cw,260
abi/report/__init__.py,sha256=5rxJlywqtJoa-fgUfIWEFK1MT19s0bGm_Ui9ZcNvuC8,1858
abi/report/citations.py,sha256=KcqUDqzK_OW3b0cLcdvTefRdAGl5Z-Sgu4yN9MYrIrc,5309
abi/report/generic_report.py,sha256=067Wre0dsi40z7_dPLKx9uRDpVQpq_w-JUpDkltbIgo,13193
abi/report/html.py,sha256=t7IQrd11EGGakx6GgpP5bjNPenB9MSG1sX8pR0_Isno,9601
abi/report/limitations.py,sha256=iojvS7f9dmYhZtlmSenHGtIyGIeyhr11JUwhFVhECl4,3077
abi/report/methods.py,sha256=YnUvzfk-7DIWjXausfU5B1GTKIvKhb6pgfImS3nIX5k,6576
abi/runtimes/__init__.py,sha256=NNy-EgrIPcpnlprV3fd_VFFZUPm8V0Zc51Dgw7ZNi-w,432
abi/runtimes/base.py,sha256=x0vML-nIozrwvHV8jJL9rR7bWIcA683MHQzy_DMP5jI,1762
abi/runtimes/hpc.py,sha256=Cp9lEkTbqAzEzmAX_iQ7ynQ8NUXUgn9V4Uo95e0BzL4,15623
abi/runtimes/local.py,sha256=r9XZG6Kw9_2jTXesr6Ca3tUs1aXZUb7NuXbS7Y-B4C4,2094
abi/runtimes/nextflow.py,sha256=fjlOMn3gOkbpK9nFO-JLIjL8wQHir2b2qeFrODVq2gc,13964
abi/skills/README.md,sha256=N81pHQbh-J6RMTP67mSrN-rs-JZHjFMFoxUgu6vSWOg,12112
abi/skills/abi_agent/SKILL.md,sha256=wdkI05qpvNT61u42wdthgbgEW2oss3a20biEG8tL9Nw,9664
abi/skills/abricate/SKILL.md,sha256=UUB5cKOyiti-eWMs4-QMmWkCuSOMRPVi-hJYK7rZPHE,2406
abi/skills/amrfinderplus/SKILL.md,sha256=fNZZkXZ5JB_9meFj7OEIxHbaeRqVj9Saif7L1Mv2GJo,2192
abi/skills/autoplasm_agent/SKILL.md,sha256=oeMGyvtbeTwUI2Y-4tYRZKdXDT5XhDyCPFOeYuI5a9w,12898
abi/skills/bakta/SKILL.md,sha256=FCF0HbypbDi3KcAkDj4kO8VCOCcMVJZ0h77bKoI20KI,2325
abi/skills/blast/SKILL.md,sha256=jCoyEKWhuIvqGdFxBuajN60XEPpt2izC4ly21b-wQwI,2286
abi/skills/bowtie2/SKILL.md,sha256=xBljNAGWJt8M8qpHE_46qiZOhvAcB8HHYhfnnIfBY98,2456
abi/skills/clinker/SKILL.md,sha256=5l0JFsN6edvHRAPXNMYqxqk-pGURZsA4Ii408Y2O85E,2231
abi/skills/copla/SKILL.md,sha256=hTpsdpwgA814r-SUMzEvePGz70So89VvubjQXoOEiSc,2304
abi/skills/coverm/SKILL.md,sha256=0EFeNo3zY0SVusrdikVilf3w1gOMaBSVlLv1f3fpHxA,2233
abi/skills/fastp/SKILL.md,sha256=0b3vPJsBkjXuWkLeX0ypVPndt73GevgFOPdWf-ZW6ps,2963
abi/skills/fastplong/SKILL.md,sha256=3LPS56g5RBX6_yz9ub8arcNgl_If4MxTuvdKFadxyWg,2451
abi/skills/fastqc/SKILL.md,sha256=H8wc_HWWKdWAJBD599nEjK8ttuJ0E5LZ0BC2EmcwmH4,2146
abi/skills/fastspar/SKILL.md,sha256=2ex8FvrigleKTkvFlNEo5NmTwj7bRY9nSonwAyvPAD4,2351
abi/skills/filtlong/SKILL.md,sha256=0T4GKJ4A6P7T-PS_lCQNaHBVjU3ftot4yTDEpilp0pg,2138
abi/skills/genomad/SKILL.md,sha256=LAGKXi2tatuBSn69vTaYnQCTFp4vKWylYJEJCPBa220,2401
abi/skills/gplas2/SKILL.md,sha256=YbRMV7azxfgVgGRyvRwAefkv3NZZhVaanaGF-Ch_7Ys,2346
abi/skills/hifiadapterfilt/SKILL.md,sha256=GuISnx0As0S38WCueQ9dA1nCFYX5z4nnZK3sOzbpVYQ,2348
abi/skills/hifiasm_meta/SKILL.md,sha256=Ie-kSIaLZSyuzK9eHbgWutZ_Wi6HlBzPovXwbASCoH0,2584
abi/skills/integronfinder/SKILL.md,sha256=Xm18omrS9T8chcRYfZ5eBqNE0djSoU2NYNaI0-jD8pk,2380
abi/skills/isescan/SKILL.md,sha256=a9VhYtmiUXEWwj588cq8hHmZk8-CvJ9PPF1W_LSNpAI,2161
abi/skills/kraken2/SKILL.md,sha256=koV5FXpu1NfeaGWBuGzP7LySDl41KF9wRXI4d6apVeY,2418
abi/skills/megahit/SKILL.md,sha256=0X_Dy2sZOWiXFYlvc5isua0gf41pDgy2intxuCO7RHk,2469
abi/skills/metaflye/SKILL.md,sha256=0tb6sHAsyMX2Fih3bjNSjhcKUzHgGx2SzmlR8oVmCiM,2412
abi/skills/metaphlan/SKILL.md,sha256=1coYZlxizvBeYOudsOI1KyqQI3G-XsZp8kmNMYOAGlE,2817
abi/skills/metaspades/SKILL.md,sha256=qW1Nf8H7DRInHjUdWiIjtVfLcqCzCzLdRyOpKP5RSMU,2299
abi/skills/minimap2/SKILL.md,sha256=Q7Y4IHGmAs2rBXfnDvf44qR80ZjjEAgkDWt1bfkY_3A,2357
abi/skills/mmseqs2/SKILL.md,sha256=ORP25LzmTGZUnAVh4WrRyREwVGpD5SuUhKHYoSsP5TQ,2266
abi/skills/mob_suite/SKILL.md,sha256=hy_IaEjspflaXH2HZsokOLQv_STBIDQvymfJ4kZR_Os,3036
abi/skills/multiqc/SKILL.md,sha256=okU8n-8M9IAs1H-Lx1zDLIoMNJJ72w7kDTeaErU--bE,1929
abi/skills/mummer/SKILL.md,sha256=l5z20pXuhfJLlqyZcfdughEW88iw4lX9wIPXczIK2z8,2352
abi/skills/nanoplot/SKILL.md,sha256=6AXwEOL_0FE78W00O9S1Uu0TK24-n8fOn_C_6OxZAy0,2146
abi/skills/opera_ms/SKILL.md,sha256=T9EzQ_hmam3Y5YHNXbdGTLVIP2I1D9N3_Dbz0j8-Fbw,2583
abi/skills/plasmaag/SKILL.md,sha256=-YhDkdV5THo-JetyYOVNPlA9MyTzS3oO9e4mVKXWBvM,2610
abi/skills/plasme/SKILL.md,sha256=Ea1oBc5PiFBCyuuTY95t2wOtZ_KEB22o5fSNZadYjHE,2355
abi/skills/plasmidfinder/SKILL.md,sha256=D3mbKYkGYoCd0UxjutgIKZZui-6Y7vs3r6kUdtMVDe4,2381
abi/skills/plasmidhostfinder/SKILL.md,sha256=YoXKVd9HPi_3n-_FyLVA44Hhec1xrMQ2st-i_5qXhTM,2367
abi/skills/plasx/SKILL.md,sha256=oUKrUdvwgx2MRyiiHqWoAP4-BR5iyKh3XVO8T6wds4Q,2360
abi/skills/quast/SKILL.md,sha256=6J-eO5apikWpsY-xlZeynE63TM3J3tAk8ddOqvJztZA,2142
abi/skills/report_markdown/SKILL.md,sha256=zW-QWqrD57NsWJ3rQ7uBf24YCUcCD82ZdzFEfDWp-Q4,2146
abi/skills/samtools/SKILL.md,sha256=nstn1C6aOqLwVtHyrOrI7updOSRtPWCKPVGIeNZOfow,2125
abi/testing/__init__.py,sha256=GppnxOWho2fui0HZMs8jhSowsSKeA_r_dQKeXp5zrD4,2563
abi/testing/benchmark.py,sha256=Te3htey2TlMehSpi4VLdQsaU8xY3WYF-FePfhUU1y_8,12726
abi/workflow/__init__.py,sha256=XFlacNO2rlxxoWIJPrXZt7rBs3eHzl76X_oOY7LNSwE,1129
abi/workflow/figure_specs.py,sha256=DSMO5doZYsrIZmbpUuJG_mnSRe5c6cOhHl9D6TbDQIk,2761
abi/workflow/manifest.py,sha256=iUpQXGupZS9KoG0mFbCZrrJO4JAAN_TU_nIBfI2aweI,8459
abi/workflow/validation.py,sha256=RCHlx8ZDobcXp_xmC17VUJHShz9bha-pekDqEUpuV6s,6090
config/default.yaml,sha256=Sg5xjsuVtceKrZF2GHHsyB7PafRYYtJDH_kjiLwKnPk,2382
config/schema.yaml,sha256=IMjlZCAhD0wiDxhfNf7PInzHxhII-6GeZ4v-0XJYkgQ,1276
config/tool_registry.yaml,sha256=k0T0LQetomgOgWBE1lxXFdobAjbFEeIRunqkfx3VbJE,14740
config/profiles/dry_run.yaml,sha256=CgNh5wZazf08jBJ1yw0f0DOOyEy8YBTgBgwyLrQsQ20,59
config/profiles/hpc_slurm.yaml,sha256=N-Azc0FZSBEkK2hHzm7wkwrvGT1fhsZfA2GLzHGL6tA,124
config/profiles/local.yaml,sha256=JwS1I6hfXQrwt3TwW7-pR0eXsQ3ISvC7P38Z-h6u1-U,44
config/resource_profiles/dev_small.yaml,sha256=oc2lrSSLszHN2wDk9V-C6RPiLb17VYJs65nBDGWTfuA,170
config/resource_profiles/hpc_large.yaml,sha256=7t3x7JdGJQEg7xz3YzuYXuvNkzptPsQBJkadNrJEO70,235
config/resource_profiles/hpc_standard.yaml,sha256=Sv6hU5f43VOu5eFb32G7bjLu_u-1qDVMoRF3tpVrHY0,189
envs/abi-qc.yml,sha256=FaavIQAztbjohercYrSB3nU7pj6uFWpWSJMeKwemcYA,144
envs/abi-stats.yml,sha256=Ql6QQbxTm7o8jeBjR8qxFlZby5i_6y2xXMrkotUqIWk,178
envs/abundance.yml,sha256=TvoOfYv9vHHKNQdgXRGGg0rfhPTcNBXY601A9garG3s,193
envs/amplicon.yml,sha256=trHsGvzhM9rA2F0fsUi-zocQQta5L9PDHXB-9NfgnMk,276
envs/annotation.yml,sha256=2wVEy40SszC4moogLqNKqFN1ODae8h_PrfYRLx7sB8c,290
envs/assembly.yml,sha256=HFDbliwDmSHGUdJFCRLGAYJGbrkvN5GEW7R1An1iZyk,209
envs/base.yml,sha256=wpSr2NZeKqSEEd11UqZMHs6IRWc3p1G_2ioTEUr3pN4,440
envs/integronfinder.yml,sha256=MaTd7nGWd_ph4EFKNg5UMqCGeDKWTnDMAcUFDRY7SEE,170
envs/nextflow.yml,sha256=MmGkgbPEuWzrzXM2ABVhY5vBaS0Kwr3pg3TFk7OWor4,116
envs/plasmid_binning.yml,sha256=KRDe3R4sjxLywyViT6Rrpw2r35hDcjjJlv-Ji8zrO3U,179
envs/plasmid_detect.yml,sha256=6gAFdE0cGzAn9AMyPa9nHSJU_oeUxmv28Vn_0D0XXAY,173
envs/qc.yml,sha256=68UbEF8RoMfgTNnJX9YNNdoV_BlUyL3-NePOqZ_pP8Q,289
envs/rnaseq.yml,sha256=wRMf5mtO4vvWLEfSj-YSacd8k8jsSkuTHrUrytI37Qo,1579
envs/stats.yml,sha256=T0UT7a34hQxE3Nr6fo6cS1RoFlaHTpQN1FRSJPwu8Kk,268
envs/visualization.yml,sha256=4eoriB0CWSMr6WwFWhgxBc3diTscEoqFb2PPySbnyJ0,288
envs/wgs.yml,sha256=4mRlLrkjffNi6svCyabnn13yEPGVIiKnj_4pZkZLLTU,227
examples/config_assembly_full_run.yaml,sha256=quPlXvYN1Olq-Th754R0blRS6Ro1Toko3lWQzBCtHgU,1513
examples/config_full.yaml,sha256=zK2sPTtRA-Cln5SPur3EudLgmJy1UMUKTHd4cLlz0O8,391
examples/config_hifi_smoke.yaml,sha256=UJTdGXmI8Tf5FL-6itCl4eL5jXnThqN2VEZSUZ0I8wI,1085
examples/config_hybrid_smoke.yaml,sha256=7xt3_j_vzjNqs1FZXlMdrFJYdE_4F24xiLq76D-rkm8,1185
examples/config_illumina_smoke.yaml,sha256=XTOryqgkMHoDUTYQCeMp3_mggB7BAgLeQ1DT486POaM,1142
examples/config_minimal.yaml,sha256=vmG-6R6xF0nGNv0EMUdFZhFMrwC82YBo2goo--yA0ZA,247
examples/config_ont_smoke.yaml,sha256=r6WRGbL8d7YzY-4LtR5ujHcic6wPTQr2wzZYXiU81yA,1099
examples/sample_sheet.tsv,sha256=LeRbfcWMyl-ut4vtQVudl_3ywYsTHrBFMyoiabuGEHE,311
examples/sample_sheet_hifi.tsv,sha256=bJ01bfWYC_gtpaW5iMpOr63lJeahcSz1euEQhN66V9c,203
examples/sample_sheet_hybrid.tsv,sha256=MEkQJSJ5BmT7bKWKqgnJFFTjBsA58YIZaL1lezRiHjU,255
examples/sample_sheet_illumina.tsv,sha256=TV0Ctl2xWDcVvkir6x0yjrxu0nfFY3fUoYkwjiexWO4,219
examples/sample_sheet_ont.tsv,sha256=RRJm9YJx1V0A0VgaLzHZVUwAY-PSHJl6CGFsib8SntQ,178
examples/sample_sheet_transcriptomics.tsv,sha256=V6x0S4D9Q8WVdgAsCTO8QNeLu-dsJdZkw0pkqdQ1gV0,109
examples/fixtures/tiny_R1.fastq,sha256=LgW6r9V7wlrtj4wxA4o1ysqqpB4vBFFRLSw2q8qPEgQ,37
examples/fixtures/tiny_R2.fastq,sha256=A5_ubkQDDYzIfJgpslPHI6yT7CIqG5keeVE75YlGmDM,37
examples/fixtures/tiny_contigs.fasta,sha256=CiTwKLN2GuNReJB7f_44GXduywRt7lfp_CLeGs8bXSw,82
examples/fixtures/tiny_long.fastq,sha256=XQH0cVVO4_b3kg1ZJi82EklI1QCLYX0N8Ymaj7QR8JM,63
golden_traces/amplicon_16s.jsonl,sha256=z-XYL1GjRS6ITaQS8-XUuGtZFyJ5EuQmX3_gesfHQ_M,1373
golden_traces/metagenomic_plasmid.jsonl,sha256=k47mVHQ6D1qc8dX0eNLh75VEW9npfJ581_HbNrH8Sdg,1409
golden_traces/metatranscriptomics.jsonl,sha256=lUK7G4SVTS9GUKhGVZ9_8xGMst95ItHXbb44w-c0QUI,1208
golden_traces/rnaseq_expression.jsonl,sha256=WYJFfvkwFpi6C86rO_gbbRs3v6kTpO0NgNRF8ZlSN7o,1391
golden_traces/wgs_bacteria.jsonl,sha256=Kb3SwIcZhlxgvmz_HwgEQypUhXqzqw7-fIx4Bc1U654,1343
plugins/amplicon_16s/abi-plugin.yaml,sha256=ll72biE86hUyyfS-L1Dqrufdo0TRipYxopRvyjug_Qw,2999
plugins/amplicon_16s/citation_registry.yaml,sha256=0Ce-Ymxs7Ivp6Md5dD9YDNifsScZicTo7ECSmE9-sbY,1126
plugins/amplicon_16s/config_default.yaml,sha256=LfCpr4fg-dVdtesW3WeYEiriSinOoimc6t5o6ze4g5s,433
plugins/amplicon_16s/figure_specs.yaml,sha256=tVkr-XihCOMwy0J6WYqzTTmDhxA0wsuuefUe-kY2ekc,1322
plugins/amplicon_16s/limitations.yaml,sha256=ZTpPg74S-XB7G5lJu6UsQaLgfDjY-8kiY9KCdBKhcZs,1126
plugins/amplicon_16s/pipeline_dag.yaml,sha256=1Hlfwv0Mj0Jsu6JzdOU8O8XYQ3vQjEv08GsTEIeVyJs,5437
plugins/amplicon_16s/standard_tables.yaml,sha256=ASir4_EfT2J08G6nZMwOebMo90gXDwAJX83hD0KgInU,911
plugins/amplicon_16s/tool_registry.yaml,sha256=un4WnX1P_nIQ5xH8IZHFsU4g1wdC2UDUahqC5wZaqN8,2963
plugins/amplicon_16s/tool_contracts/cutadapt.yaml,sha256=I8leJCs7D8BhNgQbZ7RO_DU-3rZm3_gs06vS3F6h6AE,1300
plugins/amplicon_16s/tool_contracts/diversity_metrics.yaml,sha256=LSl3Lnims1TYrILOuYYtok-P75bVlJ7CwDA1_QuxlBk,1532
plugins/amplicon_16s/tool_contracts/phylogeny_build.yaml,sha256=s-Kqabtj-GCzarVhzU0dazyC0wgt61PitnqJq24HzRg,1342
plugins/amplicon_16s/tool_contracts/vsearch_denoise.yaml,sha256=N6M0whsPMfM3enyIIVRPLx8ssVU443ovMrFBmG5tbkM,972
plugins/amplicon_16s/tool_contracts/vsearch_derep.yaml,sha256=x2_zA-cSGB2D90YPbv7S27mHZkz-56NvfaeMVHFLQas,902
plugins/amplicon_16s/tool_contracts/vsearch_mergepairs.yaml,sha256=x7AgRLn643l-GcHREl8W4nM41HpzYjDdVrmc57JTK24,1160
plugins/amplicon_16s/tool_contracts/vsearch_otu.yaml,sha256=VrBH1nCwdi7FBt_IqADPm-3anNLGaTQtwJAxltN_1pE,1001
plugins/amplicon_16s/tool_contracts/vsearch_taxonomy.yaml,sha256=ldnAsig9NZbHOoYNM4j2kXrt1OzH6rOS_iyuYFHQsuc,1015
plugins/metagenomic_plasmid/README.md,sha256=xzY9G26_lv19JcJqXG3WaZVUDLxEiWlqjtRexML-kv0,609
plugins/metagenomic_plasmid/abi-plugin.yaml,sha256=HnH_VPW8IUjZbh4f3Jq4s6O8YfML42PWsw6Y6M-x06o,3488
plugins/metagenomic_plasmid/citation_registry.yaml,sha256=YbxTq6WpuHTbTH5fNod9snR91fdOKWX5M3avp2WDyg0,2523
plugins/metagenomic_plasmid/figure_specs.yaml,sha256=iLijoXKJaIfjv-x3Ni-DtRsOQQPyYYp2R8I9N5EqecU,1694
plugins/metagenomic_plasmid/limitations.yaml,sha256=VnsmqxCXVX5GzklW-0EQsqy72ZypLEq96Cg__orJATQ,1667
plugins/metagenomic_plasmid/pipeline_dag.yaml,sha256=F3C7D20pFWpXPPUSjDCU_uFsi2Cuz2yBMFodL78_D_4,66222
plugins/metagenomic_plasmid/standard_tables.yaml,sha256=MCsrTlpQKzk3Z5IFmOcFltMzzN188s1-hZ4ZxUuxEV0,2574
plugins/metagenomic_plasmid/tool_registry.yaml,sha256=s0CSXoGF4Nb3dKBP8NVOf1U0_h9LEP6wC-lUtfLZg2Y,26179
plugins/metagenomic_plasmid/tool_contracts/abricate.yaml,sha256=TBXhwYhyo0zxpdkfEUx2j-E5j0USMh49ppSnBr_oe-I,1110
plugins/metagenomic_plasmid/tool_contracts/amrfinderplus.yaml,sha256=3cD-MVZ9l-0AT-Zw7vFvmaLFq0xYWbhaHl7bFZUuzSU,956
plugins/metagenomic_plasmid/tool_contracts/bakta.yaml,sha256=IfVaQPYfF_-M75AXLGTGGA170BfnP0vYQHMwU3ZUSds,949
plugins/metagenomic_plasmid/tool_contracts/bandage.yaml,sha256=-zgksFQJg9j5KGmrM0J6avfe9uyDUBcAC1xToCBnwkA,901
plugins/metagenomic_plasmid/tool_contracts/blast.yaml,sha256=YhHUuleG9e3euS4vd5ZSpqXLbnmdyWB9-v2Q-dcjbKk,1130
plugins/metagenomic_plasmid/tool_contracts/bowtie2.yaml,sha256=6i2k_g1SRQazCI6sWBCx-qYhZzFx7By6YjkqNXRD9Ks,1198
plugins/metagenomic_plasmid/tool_contracts/bwa.yaml,sha256=SxXc_eJyvw7NHT6iL075ueYpsomf4WjKmOLnaq6Bhhg,1114
plugins/metagenomic_plasmid/tool_contracts/checkm2.yaml,sha256=c1KpSMk3COEol0oouuCsg-epXQkXM8Zea0QBYX_h8gQ,834
plugins/metagenomic_plasmid/tool_contracts/chopper.yaml,sha256=ULOn_hdT3az_JWq3Tq5s4B8PSIlwXXu7-f0wyLTHK-U,887
plugins/metagenomic_plasmid/tool_contracts/clinker.yaml,sha256=OYQERMuGHpW40Fj52rdbmCqqcYa0sOG2151qVoZwg4E,975
plugins/metagenomic_plasmid/tool_contracts/concoct.yaml,sha256=1iEojx3Uf3Px2d6fhslUJzvWx7ctEWaZszZ6w40Ca9M,968
plugins/metagenomic_plasmid/tool_contracts/conjscan.yaml,sha256=BBcUpAd-YpbgGJsICLxhjnxHPDNi_bmQkPX2EOPnDLQ,963
plugins/metagenomic_plasmid/tool_contracts/copla.yaml,sha256=uLNUZ6-C9vpV4_yslZNGmzJE9E7-XufEQzok03zLc64,1023
plugins/metagenomic_plasmid/tool_contracts/coverm.yaml,sha256=-ZjF9ctQFyShE4W5CDcAO7nLEltrIvD88Q3u7jnNxzQ,902
plugins/metagenomic_plasmid/tool_contracts/das_tool.yaml,sha256=Gs274H_58Xo4YV3gMSZTopzYYE1PyvD5tDSS5nlXTOE,1064
plugins/metagenomic_plasmid/tool_contracts/dna_features_viewer.yaml,sha256=8XbLlJfuHHr1l6sEPM_lxYnJWx2fJWdG9xaaUg2kTGQ,1132
plugins/metagenomic_plasmid/tool_contracts/eggnog_mapper.yaml,sha256=M2dVoeOgdUcTVqSB9yMvRzNPHLnxmggy7km4JNB3CQM,1076
plugins/metagenomic_plasmid/tool_contracts/fastp.yaml,sha256=7kXKK3eoVQFcmDY_lz-Q6UsspeTrKTRzd2uW2-Ij4rI,1295
plugins/metagenomic_plasmid/tool_contracts/fastplong.yaml,sha256=yjHbVwJwc8-Av7xrJPyPPHWEWP3b57JNyIbOTqJCVUg,932
plugins/metagenomic_plasmid/tool_contracts/fastqc.yaml,sha256=GCKiSlSSm5NOwncO94iH82EbNmJfcy-Wr55OW_6uR6Q,927
plugins/metagenomic_plasmid/tool_contracts/fastspar.yaml,sha256=u0BbR6WP43W1z_cCKKbgaVQO8dsT9w4rxzAHmkrp6vw,1025
plugins/metagenomic_plasmid/tool_contracts/filtlong.yaml,sha256=iQBnINApSzHau26V5LB0wdKZ-MOtn7IQWGdFk_BTf28,926
plugins/metagenomic_plasmid/tool_contracts/genomad.yaml,sha256=1fcdKZSKWLH3LZgz9uHHjySutUa-t5C0mzDnTbEleYo,1046
plugins/metagenomic_plasmid/tool_contracts/gplas2.yaml,sha256=AVnVXFDHJcWJ3Bel41nzfvLvVrUH1HMjOWg8Omcb8Fo,1043
plugins/metagenomic_plasmid/tool_contracts/gtdbtk.yaml,sha256=fIQl_E2XstKpp7S3eS6pAEZ-N0wgylpmDwy-eQ6lobo,931
plugins/metagenomic_plasmid/tool_contracts/hic_evidence.yaml,sha256=JGlSIbEGKeEzXcXXG0Qrp9_WcatQ3xYNTmg43RXQUm4,998
plugins/metagenomic_plasmid/tool_contracts/hifiadapterfilt.yaml,sha256=2mgunlNM8pI5z00rEJrfAzc3X4lsCZnl_ob9G3KSMBk,1215
plugins/metagenomic_plasmid/tool_contracts/hifiasm_meta.yaml,sha256=I6MwrF45IGVc2sZVN-TkgBa3mjazc7ewD5k4yGKt9W8,1167
plugins/metagenomic_plasmid/tool_contracts/hybridspades.yaml,sha256=kVC_9L1Mgf5KdPYPsucYvHALv-MXeTG9PI_MUSiC0Ps,1009
plugins/metagenomic_plasmid/tool_contracts/integronfinder.yaml,sha256=k9v7h2tFdQtzDnQb2t6Ra5hOGf8c00HIPZnkn1pcfoc,822
plugins/metagenomic_plasmid/tool_contracts/isescan.yaml,sha256=-zMD_QVEh0DUFLntY5z6cQuoReyXpw-vkUkXEB6LcPE,783
plugins/metagenomic_plasmid/tool_contracts/kneaddata.yaml,sha256=vGxYE8YrqWxV7A-TzNpZFrBw4_pTQKgDoxOsHzNEXiY,1058
plugins/metagenomic_plasmid/tool_contracts/kraken2.yaml,sha256=WftoAUzNNcoAL5_PAqS4LEwxvbSwI5C3J1yeT68D3nI,1140
plugins/metagenomic_plasmid/tool_contracts/macsyfinder.yaml,sha256=46bGHcGaqiN7X4xAp8BaLeNCJjtmflJI3InFicU-Uvg,934
plugins/metagenomic_plasmid/tool_contracts/maxbin2.yaml,sha256=gXdNCEqjnEMorsespMD8sTKiBGeELWjlXAp4zgq41CY,1120
plugins/metagenomic_plasmid/tool_contracts/megahit.yaml,sha256=qauYu6hun4FR_8rtSRer_49QUO7BLh5Gls_QG-3_OWU,991
plugins/metagenomic_plasmid/tool_contracts/metabat2.yaml,sha256=ieSGbJibpjxl6aOxasC3fu3w11A_0YJdt2727oYIE88,1007
plugins/metagenomic_plasmid/tool_contracts/metaflye.yaml,sha256=kcrPxdY6rX5EfKeHxwKzMB9VsD8UYl9oyoXhiCuvjDU,968
plugins/metagenomic_plasmid/tool_contracts/metaphlan.yaml,sha256=kwC5-6kgonVa3idfauFvCjp8ZfRuAFczsYGIsq-9ixA,1058
plugins/metagenomic_plasmid/tool_contracts/metaspades.yaml,sha256=s6_rG2WnoRoJs1qBMKgAHZERSqfFSRuMSkOrWZpF1SA,919
plugins/metagenomic_plasmid/tool_contracts/minced.yaml,sha256=zeu1H0VB_AMOydTpZbUzs5N_PTTMaAMAkEzlBmaGYhI,981
plugins/metagenomic_plasmid/tool_contracts/minimap2.yaml,sha256=sUpYImYAAKUkbRB-Sa-qPc2difiB8gFvHHr1pUsdF9A,1001
plugins/metagenomic_plasmid/tool_contracts/mmseqs2.yaml,sha256=FhCwJNWF99k6qspAaEOF-_4lcr6moX3Td952fzSQ7io,1137
plugins/metagenomic_plasmid/tool_contracts/mob_suite.yaml,sha256=fta0QvZ_7Z7K5pNo-eXWAnzVax-shoZG9resStrwoEI,1110
plugins/metagenomic_plasmid/tool_contracts/mob_typer.yaml,sha256=NdSuHH17xKl9Mu87xVPD02HXXktSWPn9yX-2hBRbzZ8,1024
plugins/metagenomic_plasmid/tool_contracts/multiqc.yaml,sha256=vrirxPLRH_oaojRqNhQM4G9eKJYCWBOv0XY3Dz6g-2s,746
plugins/metagenomic_plasmid/tool_contracts/mummer.yaml,sha256=68s-9psO5QzKruIMG1f4_c-PA8k22ZiADWWyZhIhnxo,1068
plugins/metagenomic_plasmid/tool_contracts/nanoplot.yaml,sha256=PDsswRK-VSQ_El5cqOI_mDNd1JWMMIsGRwi1s2-fdkE,937
plugins/metagenomic_plasmid/tool_contracts/opera_ms.yaml,sha256=M8GOBtSJQZ65cnXkD6SBHLSdQp1pRMUjJa7PeVVGLQk,1287
plugins/metagenomic_plasmid/tool_contracts/plasmaag.yaml,sha256=rVRdbfwUTwV4BHwpaQdIDxOQPdoXIDO91_ypEjmj-uk,1036
plugins/metagenomic_plasmid/tool_contracts/plasme.yaml,sha256=bkRKCL3nXvXmM0Ggn3ZUvsvOFyMu_MJ55S08BkfIeCo,1096
plugins/metagenomic_plasmid/tool_contracts/plasmidfinder.yaml,sha256=W5GKTe-7VKy78E_j9v6h6YN3sogvr03J9bOwqzRjTDU,1000
plugins/metagenomic_plasmid/tool_contracts/plasmidhostfinder.yaml,sha256=-EK2yt-KkH3Y7yBtnLSD2mFoD9do-a_W8Z7L1YZB12c,1165
plugins/metagenomic_plasmid/tool_contracts/plasx.yaml,sha256=ITs9bg2NBRudA-J6xijfhUC0dCQLNALbolYAkDyE5xA,1112
plugins/metagenomic_plasmid/tool_contracts/platon.yaml,sha256=LIqy3zEut4hLMHmWs5NFRS4k6-nAFZKbzA-AsF684Bo,1002
plugins/metagenomic_plasmid/tool_contracts/pmlst.yaml,sha256=WZFBwl8pYWL3MXgaNKH0XuWMIuZoeYZkcCA-hBpBjHM,909
plugins/metagenomic_plasmid/tool_contracts/porechop.yaml,sha256=JWKWdJ-XvLAjMDWeTCkUlBRVKys2FKpU93svyuMEAPg,879
plugins/metagenomic_plasmid/tool_contracts/prodigal.yaml,sha256=8I-sT9WI6veTwn3P0R6j5GLV9cJcqWh_7bK1QCQYacY,1095
plugins/metagenomic_plasmid/tool_contracts/pycirclize.yaml,sha256=qkh8cB_qyjpGi8SLCyBcGO-OV9ikPROmPwzPCp8ZRnE,1260
plugins/metagenomic_plasmid/tool_contracts/pyvis.yaml,sha256=qAeFxdFvPlHZCavmzhIMAwCC3k1f2Ac16UUfv3ugwlQ,1085
plugins/metagenomic_plasmid/tool_contracts/quast.yaml,sha256=Ksay1He2v3Qr9Zozk0jh71bE2oM3z2x-t7AEGNl1uQU,834
plugins/metagenomic_plasmid/tool_contracts/recycler.yaml,sha256=nop9mkjGjDKR-oVBnW2qYuhnSqcW0bXirx-KadpjIFs,995
plugins/metagenomic_plasmid/tool_contracts/report_markdown.yaml,sha256=DTIuC7fosbhtXSd7ABuB3xMAYmmAU2GU_Sb7f6c99s0,721
plugins/metagenomic_plasmid/tool_contracts/rgi.yaml,sha256=hRsawTjfKzgJ4rzzSOADlLc40Hrc-_T2OgzrUK16Nuc,1049
plugins/metagenomic_plasmid/tool_contracts/samtools.yaml,sha256=DbPc9jwSKrNvaObQ7-YhHpciuCzbpc5yQWp8WQEeqg4,731
plugins/metagenomic_plasmid/tool_contracts/scapp.yaml,sha256=XmzLgQODHYAcZAGKu6dG6EACqiRfjSdPecybb6UGWik,976
plugins/metagenomic_plasmid/tool_contracts/semibin.yaml,sha256=hfyzzqvoE9vfC8CNzSh2Vcy7X6bYYRgUZ766mr2c13A,979
plugins/metatranscriptomics/abi-plugin.yaml,sha256=1yLUC0urkmt3XKLdlHVSFLP8NI6wgLHM4M1JnY_D26Y,2234
plugins/metatranscriptomics/citation_registry.yaml,sha256=4DHPoi6xhiZabdxhwKSqueDhPoFPOC-iZm5CHYwkGCA,1055
plugins/metatranscriptomics/config_default.yaml,sha256=k5QHMs7mZEFz1gbSLcw2Q9dUiHFB1LSUI74941eySE4,415
plugins/metatranscriptomics/figure_specs.yaml,sha256=Bvi7nET3h08lRY3JMCHzBwKCxV2wHe8WOiCrvVtCrbA,1203
plugins/metatranscriptomics/limitations.yaml,sha256=fyj8DX94gxaz0H_prRWvylXkQtONYVzVZ1iY9HpxtXc,1555
plugins/metatranscriptomics/sample_sheet_template.tsv,sha256=V6x0S4D9Q8WVdgAsCTO8QNeLu-dsJdZkw0pkqdQ1gV0,109
plugins/metatranscriptomics/standard_tables.yaml,sha256=-sTQ7H6vxh-AoGu8zMJew5SmrA_Ix8xWr236VMTpzL0,305
plugins/metatranscriptomics/tool_registry.yaml,sha256=f-cavAu7UIgV9lYhpXzNvk8-LAopK-PZK_F30LYox_g,1681
plugins/metatranscriptomics/skills/fastp/SKILL.md,sha256=-Dz-iv9nCXM_LayYAtiMTLvk6O3h7AExI8RsnqkPibM,1133
plugins/metatranscriptomics/skills/featurecounts/SKILL.md,sha256=g2DuDQrVHtGuSnH3s0HfKVZcVdjFwzIoifV7xYIg1Sk,774
plugins/metatranscriptomics/skills/hisat2/SKILL.md,sha256=P72OqJ6aZjIt4jA6vFBJxJMGNtqF-9Uus5BYLbHVSPY,801
plugins/metatranscriptomics/skills/star/SKILL.md,sha256=Pg6pj-XuALU4bsoIzsvsctT8-2cTKB93g8MO1kyHRMM,906
plugins/metatranscriptomics/tool_contracts/fastp.yaml,sha256=agEAAygf5hLK7dVltOJE5N8Vp9YDhSstqZRXOKQM0tg,1363
plugins/metatranscriptomics/tool_contracts/featurecounts.yaml,sha256=ipcIAsp0j0ru13-nUJkID1DxYM7Q0pHqYXmS_jv9JL4,1190
plugins/metatranscriptomics/tool_contracts/hisat2.yaml,sha256=4x3DohzwkOfH4yPYmdfT5wMvGpGyctCr8wGikD8MO6A,1099
plugins/metatranscriptomics/tool_contracts/star.yaml,sha256=1V3dvaFDQU5eaEKmx2ctUIIZStif5F_nyBb9h7DiCac,1138
plugins/rnaseq_expression/abi-plugin.yaml,sha256=8OKdvTLvJ1p9V9939wqmSf35g9n-1XAbQMxws9bez8c,2264
plugins/rnaseq_expression/citation_registry.yaml,sha256=_uTVMndt-LOpBHFY_L4KyU3w6lwXAAQXeIrq-HZpMQE,991
plugins/rnaseq_expression/config_default.yaml,sha256=rMMPoibaGVGbe4lyRMcKn6GcolIGa3ex-yrhJSq6b9U,376
plugins/rnaseq_expression/figure_specs.yaml,sha256=stEt_C-SrgPxbIkgBEG8PXItUmo1JC3j3F5gS-LzDzY,2143
plugins/rnaseq_expression/limitations.yaml,sha256=e9RKQtMHBeX19RhOtDvF9vKcOZYSYsY3cfTTyUA4L10,1074
plugins/rnaseq_expression/pipeline_dag.yaml,sha256=CFpC2-151GdiLPMbz3QQEPC57xzMZIs7CEr5V_gNuQ4,4046
plugins/rnaseq_expression/sample_sheet_template.tsv,sha256=OYKfv2D1X8W6pMil18UYbm8PciK9v0J9mJP0MZchM2U,375
plugins/rnaseq_expression/standard_tables.yaml,sha256=54dR0LxcV0JFbyLxRggyqEBvhZB_w6wi1giEkr9z6O4,815
plugins/rnaseq_expression/tool_registry.yaml,sha256=3orVPYLHd1z53AdYpGoMvgq7EKvErIzq5nsQOXvI5YA,2242
plugins/rnaseq_expression/scripts/build_count_matrix.py,sha256=7sZyWgDJFJcIXZWbIQ2RyJPpWYsVusVqieGOPyxK6xE,6060
plugins/rnaseq_expression/scripts/run_deseq2.R,sha256=C_svlo_UkBoop_PY51YT79VGG2gf_seswCMkjpBzFpE,7457
plugins/rnaseq_expression/tool_contracts/build_count_matrix.yaml,sha256=zVWA3Up_cRIIcTHRnRz80GpWUCZKCwCZJkB2-Vlup-k,1599
plugins/rnaseq_expression/tool_contracts/clusterprofiler.yaml,sha256=mQMRPhrYUdMlQtiqq34k01xriFcJMLyoDhUc04cAZes,1271
plugins/rnaseq_expression/tool_contracts/deseq2.yaml,sha256=rHIDvwmgUE2CA92ajIN5TOkDVPoPUJEjTBXg2vO6qNY,1461
plugins/rnaseq_expression/tool_contracts/fastp.yaml,sha256=qg3HZFOgZEu6KODITm6ZIRZ7_cojmdPrviNEBhEfvcY,1363
plugins/rnaseq_expression/tool_contracts/featurecounts.yaml,sha256=gts5HLH_JJt0S3NC39Fhz1km77ooK3mLMxIQFEtb9ro,1187
plugins/rnaseq_expression/tool_contracts/star.yaml,sha256=3KKAq4g626MyHWtmCRguIy2Q91djfYgwioV_kWKZSjE,1135
plugins/wgs_bacteria/abi-plugin.yaml,sha256=MTrmTu3pS9oudM-p4XusiiwCAEs8dfY6QdbdoYcc2qs,2543
plugins/wgs_bacteria/citation_registry.yaml,sha256=2sUyHC_vv1IBvJG48HIOaWJDsxcijcDccLp2HSjYY3c,1437
plugins/wgs_bacteria/config_default.yaml,sha256=NRTU4BrIgtyDX6KoRaqXKetwf36ks32_dKDF28oPDps,316
plugins/wgs_bacteria/figure_specs.yaml,sha256=eJVhPQttJrJoU1nhGnQ1rW2Wrxh-Ac9gaSkxJgLcetA,1138
plugins/wgs_bacteria/limitations.yaml,sha256=vjNxwACCppU6MR6RuKCzZ5GNugn0iFPMswyxId_yi18,1120
plugins/wgs_bacteria/pipeline_dag.yaml,sha256=LSWTZa5YSC0R8A5kW1cuIn2uh-ycegkCk1ID5HqmZYM,4030
plugins/wgs_bacteria/sample_sheet_template.tsv,sha256=SctBzKZp_TYIvd7VL7gSuleaEDGMpC87cl3ymJwWOio,227
plugins/wgs_bacteria/standard_tables.yaml,sha256=8WTv3dk9YxHaXzc49jUytqsCl4fnNw6_jGwRxV5ZQB8,922
plugins/wgs_bacteria/tool_registry.yaml,sha256=Iqd3WLwF-WejQKN0FiqzNzDRCTtZeg3O5ZLFwRiLJpg,1598
plugins/wgs_bacteria/tool_contracts/amrfinderplus.yaml,sha256=CSFKcaXu2b9QdF4w4Zzh1SQ3jBskcBKDEy_NxIZTSHY,1198
plugins/wgs_bacteria/tool_contracts/fastp.yaml,sha256=G-s1vRvZIKZOktoQFp3EZSIYoepeI_vin80L2ireas4,1360
plugins/wgs_bacteria/tool_contracts/mlst.yaml,sha256=dEB_fF6WqYzmcQiUy3Ha5yfBmFEzXkAAygpev1tx9qw,899
plugins/wgs_bacteria/tool_contracts/prokka.yaml,sha256=zXR9somRVEJJZLFosi3naXBTlgYLLZrbTOxxlBbB4Pc,1161
plugins/wgs_bacteria/tool_contracts/spades.yaml,sha256=YrC0O-CRJSCYa3MnUSTiiZtejizmLwjH35GWV7sVYwI,1063
data/examples/plasmid_refseq_smoke/NC_002127.1.fasta,sha256=hz6xFLvYv5Ira0tiCHYSiniF6yUX6nY3EeEUtBUIfqk,3438
data/examples/plasmid_refseq_smoke/NC_002483.1.fasta,sha256=9TdlPvEXxT3eCCMJlRr45o6jkjQzQVqkpLlwsCcJgVI,100641
data/examples/plasmid_refseq_smoke/NC_011977.1.fasta,sha256=t7TUt9euK9i6djCDbe9ibqqlBPL9HBJ7sUCetRy2rJQ,7752
data/examples/plasmid_refseq_smoke/dataset_manifest.json,sha256=iONm1caDk8V5-f0UhDqMg7JhfLa4BliretxNtbmUm_4,1168
data/examples/plasmid_refseq_smoke/sample_sheet.tsv,sha256=wXFRvOMiVOMrueVFm7pU3i-yK7WLG_qDSXPfFO6jtRQ,935
data/examples/rnaseq_expression/README.md,sha256=0Tx8MidPV3aKNXnPjF8SxP_J9F04EhuzdK-5Xin9bf4,1272
data/examples/rnaseq_expression/config.yaml,sha256=cdeYCW9XUwdWxm-RasO2v60Qj5QUtGznyT6Eo9MGEeg,985
data/examples/rnaseq_expression/sample_sheet.tsv,sha256=OYKfv2D1X8W6pMil18UYbm8PciK9v0J9mJP0MZchM2U,375
data/examples/wgs_bacteria/README.md,sha256=FH6JVM1ORgy8J5PIaolRDMw0llobFc4FZFZRKLiN0Uk,1334
data/examples/wgs_bacteria/config.yaml,sha256=a1b5jhLXWVh-5a4rBGEY81UZ3p2QzgQovC0IQtmcD1M,907
data/examples/wgs_bacteria/sample_sheet.tsv,sha256=SctBzKZp_TYIvd7VL7gSuleaEDGMpC87cl3ymJwWOio,227
scripts/download_databases.sh,sha256=tRctPhnYiTBLoVowEW7E97M2dUbTPmz2UcOHYtRcsVg,3900
scripts/hifiasm_gfa_to_fasta.sh,sha256=nbrJgEVl1BjGgVGDIIoY0YMdJZM5utmA2rE6-rWTln0,449
scripts/normalize_hifiadapterfilt_output.sh,sha256=xi_Y5aD_5BmAK-XwYliaqcSGYZbz0Nvj0-SXzh1v-ts,543
scripts/normalize_opera_ms_output.sh,sha256=f1tHougury1V9zEQZXkBEbcLxpJFt8USgo-jvAbgGJM,709
abi_agent-1.3.2.dist-info/METADATA,sha256=5wuS06zUytiMVKl0WELqYJeAlbGvZmU3rd9vWe7IoNk,13251
abi_agent-1.3.2.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
abi_agent-1.3.2.dist-info/entry_points.txt,sha256=ecIZhPoEaqibI2Z8eRzF9u1MfRDi91Yi4WAx1KSNcwE,465
abi_agent-1.3.2.dist-info/licenses/LICENSE,sha256=HPo0_vmSaQP2O7O0-Z3re5e0_PxqsCMOTMqAyXqyk8U,1070
abi_agent-1.3.2.dist-info/RECORD,,
