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Update nextclade dataset tags and pangolin docker version in organism…
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… parameters
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@Michal-Babins
Michal-Babins committed Dec 3, 2024
1 parent 12404d8 commit 33479a3
Showing 1 changed file with 11 additions and 11 deletions.
22 changes: 11 additions & 11 deletions workflows/utilities/wf_organism_parameters.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ workflow organism_parameters {
String sc2_org_name = "sars-cov-2"
String sc2_reference_genome = "gs://theiagen-public-files-rp/terra/augur-sars-cov-2-references/MN908947.fasta"
String sc2_gene_locations_bed = "gs://theiagen-public-files-rp/terra/sars-cov-2-files/sc2_gene_locations.bed"
String sc2_nextclade_ds_tag = "2024-07-17--12-57-03Z"
String sc2_nextclade_ds_tag = "2024-11-19--14-18-53Z"
String sc2_nextclade_ds_name = "nextstrain/sars-cov-2/wuhan-hu-1/orfs"
String sc2_pangolin_docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.29"
String sc2_pangolin_docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.31"
Int sc2_genome_len = 29903
Int sc2_vadr_max_length = 30000
Int sc2_vadr_skip_length = 10000
Expand All @@ -65,7 +65,7 @@ workflow organism_parameters {
String mpox_org_name = "MPXV"
String mpox_reference_genome = "gs://theiagen-public-files/terra/mpxv-files/MPXV.MT903345.reference.fasta"
String mpox_gene_locations_bed = "gs://theiagen-public-files/terra/mpxv-files/mpox_gene_locations.bed"
String mpox_nextclade_ds_tag = "2024-04-19--07-50-39Z"
String mpox_nextclade_ds_tag = "2024-11-19--14-18-53Z"
String mpox_nextclade_ds_name = "nextstrain/mpox/lineage-b.1"
String mpox_kraken_target_organism = "Monkeypox virus"
String mpox_primer_bed_file = "gs://theiagen-public-files/terra/mpxv-files/MPXV.primer.bed"
Expand Down Expand Up @@ -124,23 +124,23 @@ workflow organism_parameters {
if (flu_subtype == "H1N1") {
String h1n1_ha_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_ha.fasta"
String h1n1_ha_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_ha.gb"
String h1n1_ha_nextclade_ds_tag = "2024-07-03--08-29-55Z"
String h1n1_ha_nextclade_ds_tag = "2024-11-27--02-51-00Z"
String h1n1_ha_nextclade_ds_name = "nextstrain/flu/h1n1pdm/ha/MW626062"
String h1n1_ha_clades_tsv = "gs://theiagen-public-files-rp/terra/flu-references/clades_h1n1pdm_ha.tsv"
String h1n1_ha_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_h1n1pdm.json"
}
if (flu_subtype == "H3N2") {
String h3n2_ha_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_ha.fasta"
String h3n2_ha_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_ha.gb"
String h3n2_ha_nextclade_ds_tag = "2024-08-08--05-08-21Z"
String h3n2_ha_nextclade_ds_tag = "2024-11-27--02-51-00Z"
String h3n2_ha_nextclade_ds_name = "nextstrain/flu/h3n2/ha/EPI1857216"
String h3n2_ha_clades_tsv = "gs://theiagen-public-files-rp/terra/flu-references/clades_h3n2_ha.tsv"
String h3n2_ha_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_h3n2.json"
}
if (flu_subtype == "Victoria") {
String vic_ha_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_vic_ha.fasta"
String vic_ha_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_vic_ha.gb"
String vic_ha_nextclade_ds_tag = "2024-07-03--08-29-55Z"
String vic_ha_nextclade_ds_tag = "2024-11-05--09-19-52Z"
String vic_ha_nextclade_ds_name = "nextstrain/flu/vic/ha/KX058884"
String vic_ha_clades_tsv = "gs://theiagen-public-files-rp/terra/flu-references/clades_vic_ha.tsv"
String vic_ha_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_vic.json"
Expand All @@ -167,21 +167,21 @@ workflow organism_parameters {
if (flu_subtype == "H1N1") {
String h1n1_na_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_na.fasta"
String h1n1_na_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_h1n1pdm_na.gb"
String h1n1_na_nextclade_ds_tag = "2024-07-03--08-29-55Z"
String h1n1_na_nextclade_ds_tag = "2024-11-05--09-19-52Z"
String h1n1_na_nextclade_ds_name = "nextstrain/flu/h1n1pdm/na/MW626056"
String h1n1_na_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_h1n1pdm.json"
}
if (flu_subtype == "H3N2") {
String h3n2_na_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_na.fasta"
String h3n2_na_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_h3n2_na.gb"
String h3n2_na_nextclade_ds_tag = "2024-04-19--07-50-39Z"
String h3n2_na_nextclade_ds_tag = "2024-11-05--09-19-52Z"
String h3n2_na_nextclade_ds_name = "nextstrain/flu/h3n2/na/EPI1857215"
String h3n2_na_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_h3n2.json"
}
if (flu_subtype == "Victoria") {
String vic_na_reference = "gs://theiagen-public-files-rp/terra/flu-references/reference_vic_na.fasta"
String vic_na_reference_gbk = "gs://theiagen-public-files-rp/terra/flu-references/reference_yam_na.gb"
String vic_na_nextclade_ds_tag = "2024-04-19--07-50-39Z"
String vic_na_nextclade_ds_tag = "2024-11-05--09-19-52Z"
String vic_na_nextclade_ds_name = "nextstrain/flu/vic/na/CY073894"
String vic_na_auspice_config = "gs://theiagen-public-files-rp/terra/flu-references/auspice_config_vic.json"
}
Expand All @@ -197,7 +197,7 @@ workflow organism_parameters {
if (organism == "rsv_a" || organism == "rsv-a" || organism == "RSV-A" || organism == "RSV_A") {
String rsv_a_org_name = "rsv_a"
String rsv_a_reference_genome = "gs://theiagen-public-files-rp/terra/rsv_references/reference_rsv_a.fasta"
String rsv_a_nextclade_ds_tag = "2024-08-01--22-31-31Z"
String rsv_a_nextclade_ds_tag = "2024-11-27--02-51-00Z"
String rsv_a_nextclade_ds_name = "nextstrain/rsv/a/EPI_ISL_412866"
Int rsv_a_genome_len = 15500
String rsv_a_kraken_target_organism = "Respiratory syncytial virus"
Expand All @@ -221,7 +221,7 @@ workflow organism_parameters {
if (organism == "rsv_b" || organism == "rsv-b" || organism == "RSV-B" || organism == "RSV_B") {
String rsv_b_org_name = "rsv_b"
String rsv_b_reference_genome = "gs://theiagen-public-files-rp/terra/rsv_references/reference_rsv_b.fasta"
String rsv_b_nextclade_ds_tag = "2024-08-01--22-31-31Z"
String rsv_b_nextclade_ds_tag = "2024-11-27--02-51-00Z"
String rsv_b_nextclade_ds_name = "nextstrain/rsv/b/EPI_ISL_1653999"
Int rsv_b_genome_len = 15500
String rsv_b_kraken_target_organism = "Human orthopneumovirus"
Expand Down

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