From 5bf1eadad9cf81a6b8c08635ab278b5b0d69ceab Mon Sep 17 00:00:00 2001 From: Danny Park Date: Thu, 25 Mar 2021 13:40:32 -0400 Subject: [PATCH] make standalone sarscov2_sequencing_reports workflow accept multiple runs of input --- .../workflows/sarscov2_sequencing_reports.wdl | 25 ++++++++++++++++--- 1 file changed, 22 insertions(+), 3 deletions(-) diff --git a/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl b/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl index 55b0076fa..45a1a73c5 100644 --- a/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl +++ b/pipes/WDL/workflows/sarscov2_sequencing_reports.wdl @@ -1,16 +1,35 @@ version 1.0 import "../tasks/tasks_sarscov2.wdl" as sarscov2 +import "../tasks/tasks_reports.wdl" as reports workflow sarscov2_sequencing_reports { meta { description: "Produce per-state and per-collaborator weekly reports of SARS-CoV-2 surveillance data." } - call sarscov2.sequencing_report + input { + Array[File] assembly_stats_tsvs + String max_date + } + + call reports.tsv_join { + input: + input_tsvs = assembly_stats_tsvs, + id_col = 'sample', + out_basename = 'assembly_stats-cumulative-~{max_date}' + } + + call sarscov2.sequencing_report { + input: + assembly_stats_tsv = tsv_join.out_tsv, + max_date = max_date + } output { - Array[File] sequencing_reports_pdfs = sequencing_report.reports - Array[File] sequencing_reports_xlsxs = sequencing_report.sheets + File assembly_stats_cumulative_tsv = tsv_join.out_tsv + Array[File] sequencing_reports_pdfs = sequencing_report.reports + Array[File] sequencing_reports_xlsxs = sequencing_report.sheets + File sequencing_reports_zip = sequencing_report.all_zip } }