diff --git a/tasks/species_typing/task_pangolin.wdl b/tasks/species_typing/task_pangolin.wdl index 737faa1cc..be464360e 100644 --- a/tasks/species_typing/task_pangolin.wdl +++ b/tasks/species_typing/task_pangolin.wdl @@ -6,7 +6,7 @@ task pangolin4 { String samplename Int min_length = 10000 Float max_ambig = 0.5 - String docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3-pdata-1.21" + String docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.22" String? analysis_mode Boolean expanded_lineage=true Boolean skip_scorpio=false diff --git a/tasks/task_versioning.wdl b/tasks/task_versioning.wdl index d2c02588b..82bb93e76 100644 --- a/tasks/task_versioning.wdl +++ b/tasks/task_versioning.wdl @@ -8,7 +8,7 @@ task version_capture { volatile: true } command { - PHB_Version="PHB v1.0.1" + PHB_Version="PHB v1.1.0" ~{default='' 'export TZ=' + timezone} date +"%Y-%m-%d" > TODAY echo "$PHB_Version" > PHB_VERSION diff --git a/tasks/taxon_id/task_gambit.wdl b/tasks/taxon_id/task_gambit.wdl index b9c6013cd..9c253984d 100644 --- a/tasks/taxon_id/task_gambit.wdl +++ b/tasks/taxon_id/task_gambit.wdl @@ -5,8 +5,8 @@ task gambit { File assembly String samplename String docker = "us-docker.pkg.dev/general-theiagen/staphb/gambit:0.5.0" - File? gambit_db_genomes - File? gambit_db_signatures + File gambit_db_genomes = "gs://theiagen-public-files/terra/gambit_files/1.1.0/gambit-metadata-1.1-230417.gdb" + File gambit_db_signatures = "gs://theiagen-public-files/terra/gambit_files/1.1.0/gambit-signatures-1.1-230417.gs" Int disk_size = 100 Int memory = 16 # set default Int cpu = 8 # set default @@ -20,7 +20,8 @@ task gambit { gambit --version | tee GAMBIT_VERSION # set gambit reference dir; will assume that gambit genomes and signatures will be provided by user in tandem or not at all - if [[ ! -z "~{gambit_db_genomes}" ]]; then + # -s evaluates to TRUE if the file exists and has a size greater than zero + if [[ -s "~{gambit_db_genomes}" ]]; then echo "User gabmit db identified; ~{gambit_db_genomes} will be utilized for alignment" gambit_db_version="$(basename -- '~{gambit_db_genomes}'); $(basename -- '~{gambit_db_signatures}')" gambit_db_dir="${PWD}/gambit_database" diff --git a/tests/inputs/completely-empty-for-test.txt b/tests/inputs/completely-empty-for-test.txt new file mode 100644 index 000000000..e69de29bb diff --git a/tests/inputs/theiaprok/wf_theiaprok_illumina_pe.json b/tests/inputs/theiaprok/wf_theiaprok_illumina_pe.json index 59947b1af..c5e3444a7 100644 --- a/tests/inputs/theiaprok/wf_theiaprok_illumina_pe.json +++ b/tests/inputs/theiaprok/wf_theiaprok_illumina_pe.json @@ -34,5 +34,7 @@ "theiaprok_illumina_pe.merlin_magic.cladetyper.ref_clade4_annotated" : "./tests/inputs/empty-for-test.txt", "theiaprok_illumina_pe.merlin_magic.cladetyper.ref_clade5" : "./tests/inputs/empty-for-test.txt", "theiaprok_illumina_pe.merlin_magic.cladetyper.ref_clade5_annotated" : "./tests/inputs/empty-for-test.txt", - "theiaprok_illumina_pe.bakta.bakta_db" : "./tests/inputs/empty-for-test.txt" + "theiaprok_illumina_pe.bakta.bakta_db" : "./tests/inputs/empty-for-test.txt", + "theiaprok_illumina_pe.gambit.gambit_db_signatures" : "./tests/inputs/completely-empty-for-test.txt", + "theiaprok_illumina_pe.gambit.gambit_db_genomes" : "./tests/inputs/completely-empty-for-test.txt" } diff --git a/tests/inputs/theiaprok/wf_theiaprok_illumina_pe_cromwell.json b/tests/inputs/theiaprok/wf_theiaprok_illumina_pe_cromwell.json index 440f360e8..fc91e0c5d 100644 --- a/tests/inputs/theiaprok/wf_theiaprok_illumina_pe_cromwell.json +++ b/tests/inputs/theiaprok/wf_theiaprok_illumina_pe_cromwell.json @@ -6,5 +6,7 @@ "theiaprok_illumina_pe.read_QC_trim.call_midas": false, "theiaprok_illumina_pe.genome_annotation": "prokka", "theiaprok_illumina_pe.shovill_pe.assembler": "skesa", - "theiaprok_illumina_pe.merlin_magic.call_poppunk": false + "theiaprok_illumina_pe.merlin_magic.call_poppunk": false, + "theiaprok_illumina_pe.gambit.gambit_db_signatures" : "./tests/inputs/completely-empty-for-test.txt", + "theiaprok_illumina_pe.gambit.gambit_db_genomes" : "./tests/inputs/completely-empty-for-test.txt" } diff --git a/tests/inputs/theiaprok/wf_theiaprok_illumina_se.json b/tests/inputs/theiaprok/wf_theiaprok_illumina_se.json index 570d59701..126792e6d 100644 --- a/tests/inputs/theiaprok/wf_theiaprok_illumina_se.json +++ b/tests/inputs/theiaprok/wf_theiaprok_illumina_se.json @@ -33,5 +33,7 @@ "theiaprok_illumina_se.merlin_magic.cladetyper.ref_clade4_annotated" : "./tests/inputs/empty-for-test.txt", "theiaprok_illumina_se.merlin_magic.cladetyper.ref_clade5" : "./tests/inputs/empty-for-test.txt", "theiaprok_illumina_se.merlin_magic.cladetyper.ref_clade5_annotated" : "./tests/inputs/empty-for-test.txt", - "theiaprok_illumina_se.bakta.bakta_db" : "./tests/inputs/empty-for-test.txt" + "theiaprok_illumina_se.bakta.bakta_db" : "./tests/inputs/empty-for-test.txt", + "theiaprok_illumina_se.gambit.gambit_db_signatures" : "./tests/inputs/completely-empty-for-test.txt", + "theiaprok_illumina_se.gambit.gambit_db_genomes" : "./tests/inputs/completely-empty-for-test.txt" } diff --git a/tests/inputs/theiaprok/wf_theiaprok_illumina_se_cromwell.json b/tests/inputs/theiaprok/wf_theiaprok_illumina_se_cromwell.json index 1eb1f1394..8b2ac576c 100644 --- a/tests/inputs/theiaprok/wf_theiaprok_illumina_se_cromwell.json +++ b/tests/inputs/theiaprok/wf_theiaprok_illumina_se_cromwell.json @@ -5,5 +5,7 @@ "theiaprok_illumina_se.read_QC_trim.call_midas": false, "theiaprok_illumina_se.genome_annotation": "prokka", "theiaprok_illumina_se.shovill_se.assembler": "skesa", - "theiaprok_illumina_se.merlin_magic.call_poppunk": false + "theiaprok_illumina_se.merlin_magic.call_poppunk": false, + "theiaprok_illumina_se.gambit.gambit_db_signatures" : "./tests/inputs/completely-empty-for-test.txt", + "theiaprok_illumina_se.gambit.gambit_db_genomes" : "./tests/inputs/completely-empty-for-test.txt" } diff --git a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml index 9b9e2e565..81f0b8a0a 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_clearlabs.yml @@ -250,7 +250,7 @@ - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tag.json - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tree.json - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/virus_properties.json - md5sum: 1567bbba6ac947a96db159df7fd102dd + md5sum: c0aa53e26cea703a0e7dc8d292ff5c89 - path: miniwdl_run/call-nextclade/work/nextclade_gene_E.translation.fasta md5sum: 14808ad8b34c8bac7de500707400250e - path: miniwdl_run/call-nextclade/work/nextclade_gene_M.translation.fasta @@ -318,15 +318,15 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE md5sum: 717da6cd0df2d2f1d00461f3498aaca9 - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES - md5sum: 3cf7fd185fe58af5952d52e91d4805c0 + md5sum: 59478efddde2191ead1b46b1f121bbc9 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4f37bb038d973d7e32df5cbbc4067c87 + md5sum: edfb0c7ebdbf598df19861b650ee904a - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 6c7f688ada8c1e247782758d7fca08e7 + md5sum: ef9c730f9b45d2fc284575c13fe7c920 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-pangolin4/work/clearlabs.pangolin_report.csv - md5sum: e0512d549aa89d290f6aee20b63cbb63 + md5sum: 58773dc8fca41e521ec7ab24df371365 - path: miniwdl_run/call-sc2_gene_coverage/command md5sum: e44c070a15a0f8d42348103b0440f691 - path: miniwdl_run/call-sc2_gene_coverage/inputs.json diff --git a/tests/workflows/theiacov/test_wf_theiacov_fasta.yml b/tests/workflows/theiacov/test_wf_theiacov_fasta.yml index a34695c07..c5aff1e85 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_fasta.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_fasta.yml @@ -38,7 +38,7 @@ md5sum: 6808ca805661622ad65ae014a4b2a094 - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/clearlabs.fasta.gz - path: miniwdl_run/call-nextclade/command - md5sum: 847ccfc48474456a512081b2782383dd + md5sum: b5ecaad831316b3bd8f066f1e71cc0a5 - path: miniwdl_run/call-nextclade/inputs.json - path: miniwdl_run/call-nextclade/outputs.json - path: miniwdl_run/call-nextclade/stderr.txt @@ -71,9 +71,9 @@ - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/sequences.fasta md5sum: bb6b4e9e91304a396724bcb6344b8a5d - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tag.json - md5sum: 190efe28d393f17d333b3b0e147adb4f + md5sum: 97e1309e683fbaaa839198d88cd4e2d9 - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/tree.json - md5sum: 78fa5287136e13735b6c903b6a15f0ca + md5sum: 6892e6019bf88ec571b4560d66d3acb0 - path: miniwdl_run/call-nextclade/work/nextclade_dataset_dir/virus_properties.json - path: miniwdl_run/call-nextclade/work/nextclade_gene_E.translation.fasta md5sum: dc43b1e98245a25c142aec52b29a07df @@ -139,12 +139,12 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES md5sum: 71eba5c871bca955ab2a69dbd2c3c62e - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 138848a7965e23fa45633d26abbd2aaf + md5sum: 8eb91404219a5758741f83f82e9e328d - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 6c7f688ada8c1e247782758d7fca08e7 + md5sum: ef9c730f9b45d2fc284575c13fe7c920 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.fasta.gz - path: miniwdl_run/call-pangolin4/work/fasta.pangolin_report.csv - md5sum: a46fd09018b34d6309126b812ddeb8cd + md5sum: e02c65e22296686804e2be23b6d4a696 - path: miniwdl_run/call-vadr/command md5sum: f4ad614b7ad39f28a8145cec280a93c0 - path: miniwdl_run/call-vadr/inputs.json diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml index b686f2f79..b6f1eb3d9 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml @@ -368,9 +368,9 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES md5sum: e98d2fc28664c0622f6b490433286e32 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4f37bb038d973d7e32df5cbbc4067c87 + md5sum: edfb0c7ebdbf598df19861b650ee904a - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 6c7f688ada8c1e247782758d7fca08e7 + md5sum: ef9c730f9b45d2fc284575c13fe7c920 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e # sc2 gene coverage @@ -395,7 +395,7 @@ md5sum: 60725f5d2663ca8d41955a739a154cc9 # nextclade - path: miniwdl_run/call-nextclade/command - md5sum: 2a8dd9cf4d9d3a6b10d034a44c91c4c0 + md5sum: 25c2a637dcab6e9204192a1fe6386a1b - path: miniwdl_run/call-nextclade/inputs.json contains: ["dataset_name", "dataset_tag", "genome_fasta"] - path: miniwdl_run/call-nextclade/outputs.json @@ -409,7 +409,7 @@ - path: miniwdl_run/call-nextclade/work/SRR13687078.ivar.consensus.nextclade.json - path: miniwdl_run/call-nextclade/work/SRR13687078.ivar.consensus.nextclade.tsv - path: miniwdl_run/call-nextclade/work/NEXTCLADE_VERSION - md5sum: d5f4e83525024cba7eb7489cd5209e7d + md5sum: 91a455762183b41af0d8de5596e28e7f - path: miniwdl_run/call-nextclade/work/nextclade.aligned.fasta md5sum: 59893fd3ef32062d50ded18300024734 - path: miniwdl_run/call-nextclade/work/nextclade.csv diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml index 8e08f97e1..4bf9c86be 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_se.yml @@ -319,9 +319,9 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES md5sum: 0b1f8fb5b938fe71631f61234cbf7ab3 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4f37bb038d973d7e32df5cbbc4067c87 + md5sum: edfb0c7ebdbf598df19861b650ee904a - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 6c7f688ada8c1e247782758d7fca08e7 + md5sum: ef9c730f9b45d2fc284575c13fe7c920 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e # sc2 gene coverage @@ -346,7 +346,7 @@ md5sum: f7d4aa78c0a111a35f9ed1add781d4dd # nextclade - path: miniwdl_run/call-nextclade/command - md5sum: ad061b04c32b4a3d11ee156684cac457 + md5sum: ab61d2775776460dc0464393c9e51147 - path: miniwdl_run/call-nextclade/inputs.json contains: ["dataset_name", "dataset_tag", "genome_fasta"] - path: miniwdl_run/call-nextclade/outputs.json diff --git a/tests/workflows/theiacov/test_wf_theiacov_ont.yml b/tests/workflows/theiacov/test_wf_theiacov_ont.yml index d813ac46b..2f35b38d7 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_ont.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_ont.yml @@ -224,9 +224,9 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES md5sum: 35aa27af5fb90d54561ee9d45a3163d5 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4f37bb038d973d7e32df5cbbc4067c87 + md5sum: edfb0c7ebdbf598df19861b650ee904a - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 6c7f688ada8c1e247782758d7fca08e7 + md5sum: ef9c730f9b45d2fc284575c13fe7c920 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index c92f9fe8d..cc04a9958 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -221,7 +221,7 @@ - path: miniwdl_run/call-clean_check_reads/work/_miniwdl_inputs/0/test_1.clean.fastq.gz - path: miniwdl_run/call-clean_check_reads/work/_miniwdl_inputs/0/test_2.clean.fastq.gz - path: miniwdl_run/call-gambit/command - md5sum: bb2310e55a3d567803fab009dd101fe9 + md5sum: ee3f5f8694857e5de166a905b163e155 - path: miniwdl_run/call-gambit/inputs.json contains: ["assembly", "fasta", "samplename", "test"] - path: miniwdl_run/call-gambit/outputs.json @@ -624,9 +624,9 @@ - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl md5sum: 550791ca5faf11a5f75b6be18739ae01 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 01b9f9c265b15ae776a9fe86efdf59f5 + md5sum: c178145bad99e3858a1327b3774177f3 - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl - md5sum: c7f16907ef2bde7ae0e142ae685e19da + md5sum: 21bf3c68afcc1c3bc8e70503d77911b7 - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl md5sum: f06823a409a087441c8e70e46f7dfc29 - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index 232c3b53c..e8d97318d 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -218,7 +218,7 @@ md5sum: 32c0be4fb7f3030bf9c74c0a836d4f2e - path: miniwdl_run/call-clean_check_reads/work/_miniwdl_inputs/0/test_1.clean.fastq.gz - path: miniwdl_run/call-gambit/command - md5sum: bb2310e55a3d567803fab009dd101fe9 + md5sum: ee3f5f8694857e5de166a905b163e155 - path: miniwdl_run/call-gambit/inputs.json contains: ["assembly", "fasta", "samplename", "test"] - path: miniwdl_run/call-gambit/outputs.json @@ -592,9 +592,9 @@ - path: miniwdl_run/wdl/tasks/species_typing/task_ts_mlst.wdl md5sum: 550791ca5faf11a5f75b6be18739ae01 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 01b9f9c265b15ae776a9fe86efdf59f5 + md5sum: c178145bad99e3858a1327b3774177f3 - path: miniwdl_run/wdl/tasks/taxon_id/task_gambit.wdl - md5sum: c7f16907ef2bde7ae0e142ae685e19da + md5sum: 21bf3c68afcc1c3bc8e70503d77911b7 - path: miniwdl_run/wdl/tasks/taxon_id/task_kraken2.wdl md5sum: f06823a409a087441c8e70e46f7dfc29 - path: miniwdl_run/wdl/tasks/taxon_id/task_midas.wdl diff --git a/workflows/theiacov/wf_theiacov_clearlabs.wdl b/workflows/theiacov/wf_theiacov_clearlabs.wdl index b638d81ce..f7395cb8a 100644 --- a/workflows/theiacov/wf_theiacov_clearlabs.wdl +++ b/workflows/theiacov/wf_theiacov_clearlabs.wdl @@ -31,7 +31,7 @@ workflow theiacov_clearlabs { File? reference_genome # nextclade inputs String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-06-16T12:00:00Z" + String nextclade_dataset_tag = "2023-08-17T12:00:00Z" String? nextclade_dataset_name # kraken parameters String? target_org diff --git a/workflows/theiacov/wf_theiacov_fasta.wdl b/workflows/theiacov/wf_theiacov_fasta.wdl index 376e9d013..be28c7e8d 100644 --- a/workflows/theiacov/wf_theiacov_fasta.wdl +++ b/workflows/theiacov/wf_theiacov_fasta.wdl @@ -21,7 +21,7 @@ workflow theiacov_fasta { String input_assembly_method # nextclade inputs String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-06-16T12:00:00Z" + String nextclade_dataset_tag = "2023-08-17T12:00:00Z" String? nextclade_dataset_name # qc check parameters File? qc_check_table diff --git a/workflows/theiacov/wf_theiacov_illumina_pe.wdl b/workflows/theiacov/wf_theiacov_illumina_pe.wdl index 60b787ba6..6e1ae314b 100644 --- a/workflows/theiacov/wf_theiacov_illumina_pe.wdl +++ b/workflows/theiacov/wf_theiacov_illumina_pe.wdl @@ -42,9 +42,9 @@ workflow theiacov_illumina_pe { Float consensus_min_freq = 0.6 # minimum frequency for a variant to be called as SNP in consensus genome Float variant_min_freq = 0.6 # minimum frequency for a variant to be reported in ivar outputs # nextclade inputs - String nextclade_docker_image = "nextstrain/nextclade:2.13.0" + String nextclade_docker_image = "nextstrain/nextclade:2.14.0" String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-06-16T12:00:00Z" + String nextclade_dataset_tag = "2023-08-17T12:00:00Z" String? nextclade_dataset_name # nextclade flu inputs String nextclade_flu_h1n1_ha_tag = "2023-04-02T12:00:00Z" diff --git a/workflows/theiacov/wf_theiacov_illumina_se.wdl b/workflows/theiacov/wf_theiacov_illumina_se.wdl index 00898086e..c78a67e4d 100644 --- a/workflows/theiacov/wf_theiacov_illumina_se.wdl +++ b/workflows/theiacov/wf_theiacov_illumina_se.wdl @@ -31,7 +31,7 @@ workflow theiacov_illumina_se { Int trim_window_size = 4 # nextclade inputs String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-06-16T12:00:00Z" + String nextclade_dataset_tag = "2023-08-17T12:00:00Z" String? nextclade_dataset_name # reference values File? reference_genome diff --git a/workflows/theiacov/wf_theiacov_ont.wdl b/workflows/theiacov/wf_theiacov_ont.wdl index 7b7007146..037ed8bf9 100644 --- a/workflows/theiacov/wf_theiacov_ont.wdl +++ b/workflows/theiacov/wf_theiacov_ont.wdl @@ -31,7 +31,7 @@ workflow theiacov_ont { Int min_length = 400 # nextclade inputs String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-06-16T12:00:00Z" + String nextclade_dataset_tag = "2023-08-17T12:00:00Z" String? nextclade_dataset_name # reference values File? reference_genome