Use genbank_accession column as ID column

Snakefile

@@ -1,3 +1,6 @@
+if not config:
+    configfile: "config/config_zika.yaml"
+
 rule all:
     input:
         auspice_json = "auspice/zika.json",
@@ -59,12 +62,14 @@ rule filter:
         group_by = "country year month",
         sequences_per_group = 40,
         min_date = 2012,
-        min_length = 5385
+        min_length = 5385,
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur filter \
             --sequences {input.sequences} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --exclude {input.exclude} \
             --output {output.sequences} \
             --group-by {params.group_by} \
@@ -124,13 +129,15 @@ rule refine:
     params:
         coalescent = "opt",
         date_inference = "marginal",
-        clock_filter_iqd = 4
+        clock_filter_iqd = 4,
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur refine \
             --tree {input.tree} \
             --alignment {input.alignment} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --output-tree {output.tree} \
             --output-node-data {output.node_data} \
             --timetree \
@@ -212,12 +219,15 @@ rule export:
         auspice_config = files.auspice_config,
         description = files.description
     output:
-        auspice_json = rules.all.input.auspice_json
+        auspice_json = rules.all.input.auspice_json,
+    params:
+        strain_id = config.get("strain_id_field", "strain"),
     shell:
         """
         augur export v2 \
             --tree {input.tree} \
             --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
             --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
             --colors {input.colors} \
             --auspice-config {input.auspice_config} \

config/config_zika.yaml

@@ -0,0 +1,2 @@
+strain_id_field: "genbank_accession"
+display_strain_field: "strain"

config/dropped_strains.txt

@@ -1,86 +1,87 @@
-PF13/251013_18 # reference included in config/zika_reference.gb
-AFMC_U # too basal
-AFMC_S # too basal
-Boracay/16423 # too basal
-JMB_185 # too basal
-PHL/2012/CPC_0740 # too basal
+MG827392
+KX369547 # PF13/251013_18 # reference included in config/zika_reference.gb
+KY553111 # AFMC_U # too basal
+KY962729 # AFMC_S # too basal
+KY120353 # Boracay/16423 # too basal
+KU179098 # JMB_185 # too basal
+KU681082 # PHL/2012/CPC_0740 # too basal
 VIE/Bra/2016 # too basal
-Dominican_Republic/2016/PD2 # duplicate of other strain in dataset
-GD01 # duplicate of other strain in dataset
-GDZ16001 # duplicate of other strain in dataset
-VEN/UF_2/2016 # duplicate of other strain in dataset
-ZZ_1 # duplicate of other strain in dataset
-VR10599/Pavia/2016 # export with unknown origin
-34997/Pavia/2016 # export with unknown origin
-COL/FLR_00001/2015 # duplicate of COL/FLR/2015
-COL/FLR_00002/2015 # duplicate of COL/FLR/2015
-COL/FLR_00003/2015 # duplicate of COL/FLR/2015
-COL/FLR_00004/2015 # duplicate of COL/FLR/2015
-COL/FLR_00005/2015 # duplicate of COL/FLR/2015
-COL/FLR_00006/2015 # duplicate of COL/FLR/2015
-COL/FLR_00007/2015 # duplicate of COL/FLR/2015
-COL/FLR_00008/2015 # duplicate of COL/FLR/2015
-COL/FLR_00009/2015 # duplicate of COL/FLR/2015
-COL/FLR_00010/2015 # duplicate of COL/FLR/2015
-COL/FLR_00011/2015 # duplicate of COL/FLR/2015
-COL/FLR_00012/2015 # duplicate of COL/FLR/2015
-COL/FLR_00013/2015 # duplicate of COL/FLR/2015
-COL/FLR_00014/2015 # duplicate of COL/FLR/2015
-COL/FLR_00015/2015 # duplicate of COL/FLR/2015
-COL/FLR_00016/2015 # duplicate of COL/FLR/2015
-COL/FLR_00017/2015 # duplicate of COL/FLR/2015
-COL/FLR_00018/2015 # duplicate of COL/FLR/2015
-COL/FLR_00019/2015 # duplicate of COL/FLR/2015
-COL/FLR_00020/2015 # duplicate of COL/FLR/2015
-COL/FLR_00021/2015 # duplicate of COL/FLR/2015
-COL/FLR_00022/2015 # duplicate of COL/FLR/2015
-COL/FLR_00023/2015 # duplicate of COL/FLR/2015
-COL/FLR_00024/2015 # duplicate of COL/FLR/2015
-COL/FLR_00025/2015 # duplicate of COL/FLR/2015
-COL/FLR_00026/2015 # duplicate of COL/FLR/2015
-COL/FLR_00034/2015 # duplicate of COL/FLR/2015
-COL/FLR_00035/2015 # duplicate of COL/FLR/2015
-COL/FLR_00036/2015 # duplicate of COL/FLR/2015
-COL/FLR_00038/2015 # duplicate of COL/FLR/2015
-COL/FLR_00040/2015 # duplicate of COL/FLR/2015
-COL/FLR_00041/2015 # duplicate of COL/FLR/2015
-COL/FLR_00042/2015 # duplicate of COL/FLR/2015
-COL/PRV_00027/2015 # misdated
-COL/PRV_00028/2015 # misdated
-COL/PAN_00029/2015 # misdated
-COL/PAN_00030/2015 # misdated
-BRA/2016/FC_DQ12D1 # large indel
-Brazil/2016/ZBRX8 # large indel
-Brazil/2016/ZBRX11 # large indel
-CX17 # large indel
-MEX/2016/mex27 # large indel
-MEX/2016/mex50 # large indel
-SLV/2016/ElSalvador_1055 # large indel
-USVI/20/2016 # large indel
+KU853013 # Dominican_Republic/2016/PD2 # duplicate of other strain in dataset
+KU740184 # GD01 # duplicate of other strain in dataset
+KU761564 # GDZ16001 # duplicate of other strain in dataset
+KX893855 # VEN/UF_2/2016 # duplicate of other strain in dataset
+KY927808 # ZZ_1 # duplicate of other strain in dataset
+KY003154 # VR10599/Pavia/2016 # export with unknown origin
+KY003153 # 34997/Pavia/2016 # export with unknown origin
+MF574552 # COL/FLR_00001/2015 # duplicate of COL/FLR/2015
+MF574559 # COL/FLR_00002/2015 # duplicate of COL/FLR/2015
+MF574560 # COL/FLR_00003/2015 # duplicate of COL/FLR/2015
+MF574561 # COL/FLR_00004/2015 # duplicate of COL/FLR/2015
+MF574571 # COL/FLR_00005/2015 # duplicate of COL/FLR/2015
+MF574555 # COL/FLR_00006/2015 # duplicate of COL/FLR/2015
+MF574557 # COL/FLR_00007/2015 # duplicate of COL/FLR/2015
+MF574562 # COL/FLR_00008/2015 # duplicate of COL/FLR/2015
+MF574572 # COL/FLR_00009/2015 # duplicate of COL/FLR/2015
+MF574570 # COL/FLR_00010/2015 # duplicate of COL/FLR/2015
+MF574565 # COL/FLR_00011/2015 # duplicate of COL/FLR/2015
+MF574568 # COL/FLR_00012/2015 # duplicate of COL/FLR/2015
+MF574558 # COL/FLR_00013/2015 # duplicate of COL/FLR/2015
+MF574576 # COL/FLR_00014/2015 # duplicate of COL/FLR/2015
+MF574567 # COL/FLR_00015/2015 # duplicate of COL/FLR/2015
+MF574575 # COL/FLR_00016/2015 # duplicate of COL/FLR/2015
+MF574553 # COL/FLR_00017/2015 # duplicate of COL/FLR/2015
+MF574573 # COL/FLR_00018/2015 # duplicate of COL/FLR/2015
+MF574574 # COL/FLR_00019/2015 # duplicate of COL/FLR/2015
+MF574577 # COL/FLR_00020/2015 # duplicate of COL/FLR/2015
+MF574556 # COL/FLR_00021/2015 # duplicate of COL/FLR/2015
+MF574554 # COL/FLR_00022/2015 # duplicate of COL/FLR/2015
+MF574566 # COL/FLR_00023/2015 # duplicate of COL/FLR/2015
+MF574569 # COL/FLR_00024/2015 # duplicate of COL/FLR/2015
+MF574563 # COL/FLR_00025/2015 # duplicate of COL/FLR/2015
+MF574564 # COL/FLR_00026/2015 # duplicate of COL/FLR/2015
+MF574581 # COL/FLR_00034/2015 # duplicate of COL/FLR/2015
+MF574588 # COL/FLR_00035/2015 # duplicate of COL/FLR/2015
+MF574582 # COL/FLR_00036/2015 # duplicate of COL/FLR/2015
+MF574586 # COL/FLR_00038/2015 # duplicate of COL/FLR/2015
+MF574584 # COL/FLR_00040/2015 # duplicate of COL/FLR/2015
+MF574583 # COL/FLR_00041/2015 # duplicate of COL/FLR/2015
+MF574580 # COL/FLR_00042/2015 # duplicate of COL/FLR/2015
+MF574579 # COL/PRV_00027/2015 # misdated
+MF574578 # COL/PRV_00028/2015 # misdated
+MF574585 # COL/PAN_00029/2015 # misdated
+MF574587 # COL/PAN_00030/2015 # misdated
+KY785436 # BRA/2016/FC_DQ12D1 # large indel
+KY559010 # Brazil/2016/ZBRX8 # large indel
+KY559011 # Brazil/2016/ZBRX11 # large indel
+KX986761 # CX17 # large indel
+MF801405 # MEX/2016/mex27 # large indel
+MF801424 # MEX/2016/mex50 # large indel
+MF801377 # SLV/2016/ElSalvador_1055 # large indel
+VI20_12plex # USVI/20/2016 # large indel
 USVI/21/2016 # large indel
-USVI/23/2016 # large indel
-USVI/27/2016 # large indel
-USVI/30/2016 # large indel
-USVI/32/2016 # large indel
-Thailand/1605aTw # excess divergence
-VE_Ganxian # excess divergence
-ZK_YN001 # excess divergence
-Haiti/0029/2014 # contamination present
-Haiti/0033/2014 # contamination present
-Haiti/0036/2014 # contamination present
-Haiti/0054/2014 # contamination present
-Haiti/0074/2014 # contamination present
-Haiti/0097/2014 # contamination present
-mosquito/Haiti/1682/2016 # contamination present
+VI23_12plex # USVI/23/2016 # large indel
+VI27_1d # USVI/27/2016 # large indel
+VI30_1d # USVI/30/2016 # large indel
+VI32_12plex # USVI/32/2016 # large indel
+KY126351 # Thailand/1605aTw # excess divergence
+KU744693 # VE_Ganxian # excess divergence
+KY328290 # ZK_YN001 # excess divergence
+KY415986 # Haiti/0029/2014 # contamination present
+KY415987 # Haiti/0033/2014 # contamination present
+KY415990 # Haiti/0036/2014 # contamination present
+KY415988 # Haiti/0054/2014 # contamination present
+KY415989 # Haiti/0074/2014 # contamination present
+KY415991 # Haiti/0097/2014 # contamination present
+MF384325 # mosquito/Haiti/1682/2016 # contamination present
 ZF36_36S # contamination present
-MR766 # lab strain
-Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016
-Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59
-V15555 # highly diverged
-DK # lab strain
-DK23 # lab strain
-rGZ02a/2018 # highly diverged
-rGZ02p/2018 # highly diverged
-V211784 # highly diverged
-LMM/AG5643
-Faranah/18
+MK105975 # MR766 # lab strain
+KX856011 # Aedes_sp/MEX_I_44/2016 # duplicate of Aedes_aegypti/MEX/MEX_I_44/2016
+MK028857 # Puerto_Rico/2015/PRVABC59 # duplicate of PRVABC59
+MN025403 # V15555 # highly diverged
+MT505349 # DK # lab strain
+MT505350 # DK23 # lab strain
+MW680969 # rGZ02a/2018 # highly diverged
+MW680970 # rGZ02p/2018 # highly diverged
+OK054351 # V211784 # highly diverged
+MT478034 # LMM/AG5643
+OL414716 # Faranah/18