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Upgrade to nextclade v3 & update default dataset tags #375

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merged 24 commits into from
Apr 4, 2024
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6e34d2d
added new WDL task for nextclade v3. tested w miniwdl. not added to w…
kapsakcj Mar 5, 2024
1507c6e
added common miniwdl output directories to .gitignore
kapsakcj Mar 5, 2024
734700a
update sars-cov-2 nextclade defaults; removed unnecessary nextclade_d…
kapsakcj Mar 6, 2024
c2703bf
updates to nextclade v3 task
kapsakcj Mar 6, 2024
cb84f4c
update theiacov_fasta to use nextclade v3 task. tested successfully w…
kapsakcj Mar 6, 2024
0dac722
update nextclade defaults for non-sc2 organisms. Have not tested at a…
kapsakcj Mar 6, 2024
f93e691
update to nextclade 3.3.1 and implement --verbosity flag for nextclad…
kapsakcj Mar 6, 2024
4c3c21f
updated WDL task for adding samples to nextclade ref tree. tested fin…
kapsakcj Mar 6, 2024
dc08e61
update Sample_to_ref_tree_PHB workflow: removed old inputs and made a…
kapsakcj Mar 6, 2024
cd2afec
updated theiacov_fasta_batch, ilmn pe, ilmn se, and ont to use nextcl…
kapsakcj Mar 7, 2024
477a216
update theiacov_clearlabs to use nextclade_v3. did not test with mini…
kapsakcj Mar 21, 2024
7e8e9ab
Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3
kapsakcj Mar 22, 2024
6982979
fix import path for organism_paramteters subwf in theiacov_clearlabs …
kapsakcj Mar 22, 2024
fbf0b49
shellcheck lied to me. reverting last commit
kapsakcj Mar 22, 2024
303a9b4
update theiacov_fasta CI
kapsakcj Mar 22, 2024
f89b0bd
update theiacov_clearlabs CI
kapsakcj Mar 22, 2024
ef1a6ac
update theiacov_ont CI
kapsakcj Mar 22, 2024
e654a22
re-enable theiacov_illumina_pe and se CI workflows; update them for n…
kapsakcj Mar 22, 2024
728504a
Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3
kapsakcj Mar 28, 2024
6324136
update CI
kapsakcj Mar 28, 2024
2b7470a
nextclade_v3 task: removed unused pcr_primers_csv input; added back i…
kapsakcj Apr 4, 2024
0800fa0
nextclade_addToRefTree task and wf change: remove input-pcr-primers o…
kapsakcj Apr 4, 2024
84d506a
Merge remote-tracking branch 'origin/main' into cjk-nextclade-v3
kapsakcj Apr 4, 2024
7381cb6
corrected input file type for input-ref
kapsakcj Apr 4, 2024
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corrected input file type for input-ref
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kapsakcj committed Apr 4, 2024

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joaosreis João Santos Reis
commit 7381cb67842f373e4a16acfa633b4153eb679fb6
2 changes: 1 addition & 1 deletion tasks/taxon_id/task_nextclade.wdl
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Original file line number Diff line number Diff line change
@@ -69,7 +69,7 @@ task nextclade_v3 {
File? auspice_reference_tree_json
File? gene_annotations_gff
File? nextclade_pathogen_json
String? input_ref
File? input_ref
String docker = "us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.3.1"
String dataset_name
String verbosity = "warn" # other options are: "off" "error" "info" "debug" and "trace"