Fgcz sync automation folder restructuring#37
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mcarrara-bioinfo wants to merge 4 commits intofgcz_sync_automationfrom
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Fgcz sync automation folder restructuring#37mcarrara-bioinfo wants to merge 4 commits intofgcz_sync_automationfrom
mcarrara-bioinfo wants to merge 4 commits intofgcz_sync_automationfrom
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kirschen-k
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Sep 12, 2025
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Looks good! I just noted that 2 batches are missing in the badlist in fgcz.conf and was wondering why?
| #retries=10 | ||
| # mark bad runs | ||
| badlist=MiSeq_210122_MS562_o23881_DataDelivery,Fastqc_53742_2021-01-27--15-56-09,MiSeq_210129_MS564_o23775_DataDelivery,NOV657_COV19_o24384,MiSeq_210317_MS586_ww_o24329_o24329_DataDelivery,NovaSeq_20210806_NOV873_o25679_DataDelivery,NovaSeq_20210806_NOV873_o25697_DataDelivery,Fastqc_64627_2021-12-19--17-54-32,Fastqc_64710_2021-12-22--11-02-11,NovaSeq_20211217_NOV1084_o27040_DataDelivery,NovaSeq_20211217_NOV1084_o26977,NovaSeq_20211217_NOV1084_o27023,NovaSeq_20211217_NOV1084_o27026,Fastqc_64771_2021-12-25--11-15-42,Fastqc_64774_2021-12-25--11-17-46,Fastqc_64703_2021-12-22--10-58-32,Fastqc_64706_2021-12-22--11-00-41,Fastqc_64636_2021-12-19--17-58-55,Fastqc_64713_2021-12-22--11-03-19,Fastqc_64777_2021-12-25--11-19-09,Fastqc_64630_2021-12-19--17-56-31,Fastqc_64780_2021-12-25--11-20-17,Fastqc_64633_2021-12-19--17-57-51,NovaSeq_20221007_NOV1461_o29645_DataDelivery,o34397_NextSeq_240301_NS2k-272,o34397_Fastqc_2024-03-03--23-31-04,o34397_FastqScreen_2024-03-03--23-31-24,o34220_NextSeq_240216_NS2k-265,o34220_Fastqc_2024-02-19--15-50-33,o34220_FastqScreen_2024-02-19--15-50-53,o34676_Fastqc_2024-04-08--09-00-47,o34676_FastqScreen_2024-04-08--09-01-56,o34676_NovaSeq_240405_NOV1970,o35541_Aviti_2023-10-22_AV013,o36056_Aviti_240816_AV021,o39115_Aviti_250722_AV108,o39115_Aviti_250711_AV105 | ||
| badlist=MiSeq_210122_MS562_o23881_DataDelivery,Fastqc_53742_2021-01-27--15-56-09,MiSeq_210129_MS564_o23775_DataDelivery,NOV657_COV19_o24384,MiSeq_210317_MS586_ww_o24329_o24329_DataDelivery,NovaSeq_20210806_NOV873_o25679_DataDelivery,NovaSeq_20210806_NOV873_o25697_DataDelivery,Fastqc_64627_2021-12-19--17-54-32,Fastqc_64710_2021-12-22--11-02-11,NovaSeq_20211217_NOV1084_o27040_DataDelivery,NovaSeq_20211217_NOV1084_o26977,NovaSeq_20211217_NOV1084_o27023,NovaSeq_20211217_NOV1084_o27026,Fastqc_64771_2021-12-25--11-15-42,Fastqc_64774_2021-12-25--11-17-46,Fastqc_64703_2021-12-22--10-58-32,Fastqc_64706_2021-12-22--11-00-41,Fastqc_64636_2021-12-19--17-58-55,Fastqc_64713_2021-12-22--11-03-19,Fastqc_64777_2021-12-25--11-19-09,Fastqc_64630_2021-12-19--17-56-31,Fastqc_64780_2021-12-25--11-20-17,Fastqc_64633_2021-12-19--17-57-51,NovaSeq_20221007_NOV1461_o29645_DataDelivery,o34397_NextSeq_240301_NS2k-272,o34397_Fastqc_2024-03-03--23-31-04,o34397_FastqScreen_2024-03-03--23-31-24,o34220_NextSeq_240216_NS2k-265,o34220_Fastqc_2024-02-19--15-50-33,o34220_FastqScreen_2024-02-19--15-50-53,o34676_Fastqc_2024-04-08--09-00-47,o34676_FastqScreen_2024-04-08--09-01-56,o34676_NovaSeq_240405_NOV1970,o35541_Aviti_2023-10-22_AV013,o36056_Aviti_240816_AV021 |
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Why are batches "o39115_Aviti_250722_AV108,o39115_Aviti_250711_AV105" missing?
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Those are the two batches that we need to merge: 250722 and 250711, so they are not supposed to be in the badlist, as we saw together last month.
However, they still were included in the badlist in the config file on the remote. When I pushed the changes it also updated the config file
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Adapted the process to follow the new folder structure on Euler.
Side note: configured the sync to https mode for better stability