From 3b657f15d60ddcb51d5ad795367619b42874f856 Mon Sep 17 00:00:00 2001 From: Will Vuyk Date: Thu, 23 May 2024 09:30:03 -0500 Subject: [PATCH 1/3] Changed 'As of' column to 'Latest Date Sampled' for clarity --- scripts/positivity_tally.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/positivity_tally.py b/scripts/positivity_tally.py index d9391a4..5161864 100644 --- a/scripts/positivity_tally.py +++ b/scripts/positivity_tally.py @@ -67,7 +67,7 @@ def main() -> None: latest_dates = ( df.groupby("processing_plant_state")["date_purchased"].max().reset_index() ) - latest_dates.columns = ["Processing Plant State", "As of"] + latest_dates.columns = ["Processing Plant State", "Latest Date Sampled"] ## Merge the latest dates into the "Results DataFrame" results_df = pd.merge( @@ -81,7 +81,7 @@ def main() -> None: "Total Cartons", "Negative Cartons", "Positive Cartons", - "As of", + "Latest Date Sampled", ] ] From 3bd05da470b682a14c1179c8a9fec90f6d0ee0f2 Mon Sep 17 00:00:00 2001 From: Nicholas Minor Date: Thu, 23 May 2024 11:40:38 -0500 Subject: [PATCH 2/3] adding clearer proposal instructions for git-familiar and git-unfamiliar users --- DETECTION_RESULTS.tsv | 62 +++++++++++++++++------------------ assets/proposal_template.tsv | 2 +- assets/still.schema | 1 + docs/proposal_instructions.md | 18 +++++++++- 4 files changed, 50 insertions(+), 33 deletions(-) diff --git a/DETECTION_RESULTS.tsv b/DETECTION_RESULTS.tsv index 8d0dcf2..9cf52f7 100644 --- a/DETECTION_RESULTS.tsv +++ b/DETECTION_RESULTS.tsv @@ -1,31 +1,31 @@ -sample carton date_purchased date_expiration average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed -dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 -dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 -dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14 -dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14 -dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 32.435 19 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14 -dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 33.055 13 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14 -dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 -dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 -dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30081_14 dholab_carton_0014 2024-04-24 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 -dholab_30081_15 dholab_carton_0015 2024-04-26 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 -dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14 -dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14 -dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14 -dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 33.52 10 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14 -dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14 -dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 31.17 46 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14 -dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14 -dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14 -dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 26.29 1145 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14 -dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 31.34 40 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14 -dholab_30125_1 dholab_carton_0018 2024-05-02 2024-06-04 NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE OH dholab 2024-05-14 -dholab_30125_2 dholab_carton_0018 2024-05-02 2024-06-04 NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14 -dholab_30125_3 dholab_carton_0019 2024-05-02 2024-06-17 28.97 468 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE KY dholab 2024-05-14 -dholab_30125_4 dholab_carton_0019 2024-05-02 2024-06-17 30.065 116 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14 -dholab_30125_5 dholab_carton_0021 2024-05-02 2024-06-04 26.63 3500 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE TX dholab 2024-05-14 \ No newline at end of file +sample carton date_purchased date_expiration assay average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed +dholab_30081_01 dholab_carton_0001 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 +dholab_30081_02 dholab_carton_0002 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 +dholab_30081_03 dholab_carton_0003 2024-04-24 2024-06-05 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14 +dholab_30081_04 dholab_carton_0004 2024-04-24 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE MN dholab 2024-05-14 +dholab_30081_05 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 32.435 19 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14 +dholab_30081_06 dholab_carton_0006 2024-04-24 2024-05-19 qPCR 33.055 13 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE CO dholab 2024-05-14 +dholab_30081_07 dholab_carton_0007 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30081_08 dholab_carton_0008 2024-04-24 2024-05-08 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30081_09 dholab_carton_0009 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30081_10 dholab_carton_0010 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 +dholab_30081_11 dholab_carton_0011 2024-04-24 2024-05-01 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 +dholab_30081_12 dholab_carton_0012 2024-04-24 2024-05-02 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30081_13 dholab_carton_0013 2024-04-24 2024-05-07 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30081_14 dholab_carton_0014 2024-04-24 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IA dholab 2024-05-14 +dholab_30081_15 dholab_carton_0015 2024-04-26 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE WI dholab 2024-05-14 +dholab_30114_01 dholab_carton_0016 2024-05-02 2024-05-17 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE VA dholab 2024-05-14 +dholab_30114_02 dholab_carton_0017 2024-05-02 2024-06-06 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE NY dholab 2024-05-14 +dholab_30114_03 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14 +dholab_30114_04 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 33.52 10 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14 +dholab_30114_06 dholab_carton_0020 2024-05-02 2024-06-27 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE CO dholab 2024-05-14 +dholab_30114_07 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 31.17 46 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE TX dholab 2024-05-14 +dholab_30114_08 dholab_carton_0022 2024-05-02 2024-05-16 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE UT dholab 2024-05-14 +dholab_30114_09 dholab_carton_0023 2024-05-02 2024-05-30 qPCR NA AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE IN dholab 2024-05-14 +dholab_30114_10 dholab_carton_0024 2024-05-02 2024-07-11 qPCR 26.29 1145 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE MI dholab 2024-05-14 +dholab_30114_14 dholab_carton_0005 2024-04-24 2024-06-20 qPCR 31.34 40 AVRLVS_universalflu_primers.fasta AVRLVS_universalflu_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE CO dholab 2024-05-14 +dholab_30125_1 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex FALSE OH dholab 2024-05-14 +dholab_30125_2 dholab_carton_0018 2024-05-02 2024-06-04 qPCR NA DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" FALSE OH dholab 2024-05-14 +dholab_30125_3 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 28.97 468 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE KY dholab 2024-05-14 +dholab_30125_4 dholab_carton_0019 2024-05-02 2024-06-17 qPCR 30.065 116 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta "sample spun 16,000xg, 200ul of sample supernantant +200ul lysis buffer added to MagMax wastewater ultra x96 isolation on Kingfisher Apex" TRUE KY dholab 2024-05-14 +dholab_30125_5 dholab_carton_0021 2024-05-02 2024-06-04 qPCR 26.63 3500 DHO_influenzaAsurveillance_primers.fasta DHO_influenzaAsurveillance_probe.fasta 400ul sample added to MagMax wastewater ultra x96 isolation on Kingfisher Apex TRUE TX dholab 2024-05-14 \ No newline at end of file diff --git a/assets/proposal_template.tsv b/assets/proposal_template.tsv index 3322d3e..c3ee7bc 100644 --- a/assets/proposal_template.tsv +++ b/assets/proposal_template.tsv @@ -1 +1 @@ -sample carton date_purchased date_expiration average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed \ No newline at end of file +sample carton date_purchased date_expiration assay average_cycle_threshold average_copies_per_uL primer_asset_file probe_asset_file RNA_extraction_method positive_for_HPAI processing_plant_state SRA_bioproject SRA_accession contributors date_contributed diff --git a/assets/still.schema b/assets/still.schema index 83cb4bd..68fbbcb 100644 --- a/assets/still.schema +++ b/assets/still.schema @@ -10,6 +10,7 @@ sample: is_string() && !is_empty() && !is_missing() carton: is_string() || is_missing() || is_empty() date_purchased: is_date() && is_date_format("[2020-02-10]") date_expiration: is_date() || is_missing() || is_empty() +assay: any("qPCR", "dPCR", "other") || is_missing() || is_empty() average_cycle_threshold: is_numeric() || is_empty() || is_missing() average_copies_per_uL: is_numeric() || is_empty() || is_missing() primer_asset_file: is('REDACTED') || is_string() diff --git a/docs/proposal_instructions.md b/docs/proposal_instructions.md index 003213d..e01dc89 100644 --- a/docs/proposal_instructions.md +++ b/docs/proposal_instructions.md @@ -1,8 +1,24 @@ # Instructions for Proposals to Add New HPAI Detections to this repository +## GitHub Proposal Instructions + +This repo follows [the open-source proposal model used to designate SARS-CoV-2 lineages](https://github.com/cov-lineages/pango-designation), which involves proposing updates through GitHub issues and pull requests. + +For users who are less familiar with git and GitHub, we recommend you fill your results into the [proposal template](../assets/proposal_template.tsv) and open an issue in [the repo's Issues section](https://github.com/dholab/dairy-hpai-monitoring/issues). The maintainers will then review the issue. If your results pass review, they will be added to the proposals branch of the repo, run through our automated tests, and merged into the main branch. Eventually, these new results will be included in an official release. + +For users who are familiar with git and open source collaboration, we recommend the following steps to add data our [line list](../DETECTION_RESULTS.tsv): + +1. Clone or fork this resository. +2. `git checkout` the proposals branch. +3. Add rows with your results directly to the [line list](../DETECTION_RESULTS.tsv). +4. `git commit` and push your changes to the proposal branch. +5. Open a pull request (PR) to have your proposed additions added to the main branch. + +On pull request, a series of automated GitHub workflows will run that validate and normalize your PR, as well as regenerate the formatted README file. If all of these workflows pass, a repo maintainer will review your PR and merge if everything looks right. + ## Proposal template file -For ease of use, a template tsv file is provided here: [template file](../assets/proposal_template.tsv). +For ease of use, a template tsv file is provided here: [template file](../assets/proposal_template.tsv). ## Column Descriptions From a847f6318994a96e4de0dd62be559c9f5ad4fa45 Mon Sep 17 00:00:00 2001 From: GitHub Actions Bot Date: Thu, 23 May 2024 16:41:59 +0000 Subject: [PATCH 3/3] Updating positivity tally --- assets/positivity_tally.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/positivity_tally.tsv b/assets/positivity_tally.tsv index e0ce81d..1932194 100644 --- a/assets/positivity_tally.tsv +++ b/assets/positivity_tally.tsv @@ -1,4 +1,4 @@ -Processing Plant State Negative Cartons Positive Cartons Total Cartons As of +Processing Plant State Negative Cartons Positive Cartons Total Cartons Latest Date Sampled CO 1 2 3 2024-05-02 IA 5 0 5 2024-04-24 IN 1 0 1 2024-05-02