report making workflows #226

dpark01 · 2021-03-06T14:02:36Z

create new file tasks_terra.wdl and move a lot of terra-specific WDL code into here in order to make it explicit what is portable and what is not
rename workflow update_data_table to terra_update_assemblies
add a few more columns of reportable output to the assemblies_tsv file produced by sarscov2_illumina_full
create new sarscov2_sequencing_reports workflow that runs the assemblies_tsv through rmarkdown to produce weekly PDF reports for collaborators and state DPH/DOH's

…rra_table_to_tsv which downlaods a terra table

dpark01 added 9 commits March 4, 2021 19:58

move terra-specific tasks into new task file: tasks_terra.wdl

efd0bfe

rename update_data_tables to terra_update_assemblies and add a new te…

4130579

…rra_table_to_tsv which downlaods a terra table

forgot table_name input

60562d4

add index col to output

a3a0cdd

add output for vcf from reference

f8ef6f5

begin a pdf report on sequencing

faf6158

first attempt at reporting wdl task

e9dd267

add boilerplate workflow

5a37241

Merge branch 'master' into dp-reports

7b02b8d

dpark01 merged commit 294267a into master Mar 6, 2021

dpark01 deleted the dp-reports branch March 6, 2021 23:31

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