From aca9160798aa390691a1179e83b7cb818e90a8d1 Mon Sep 17 00:00:00 2001 From: kevinlibuit Date: Mon, 15 Mar 2021 04:56:11 +0000 Subject: [PATCH] update documentation --- ...dl => wf_sarscov2_nextstrain_modified.wdl} | 8 +++--- workflows/wf_titan_augur_run.wdl | 26 +++++++++---------- 2 files changed, 17 insertions(+), 17 deletions(-) rename workflows/{wf_sarscov2_nextstrain_noSub.wdl => wf_sarscov2_nextstrain_modified.wdl} (95%) diff --git a/workflows/wf_sarscov2_nextstrain_noSub.wdl b/workflows/wf_sarscov2_nextstrain_modified.wdl similarity index 95% rename from workflows/wf_sarscov2_nextstrain_noSub.wdl rename to workflows/wf_sarscov2_nextstrain_modified.wdl index 02801e2d..d5f19dfc 100644 --- a/workflows/wf_sarscov2_nextstrain_noSub.wdl +++ b/workflows/wf_sarscov2_nextstrain_modified.wdl @@ -4,11 +4,11 @@ import "../tasks/tasks_nextstrain.wdl" as nextstrain import "../tasks/tasks_reports.wdl" as reports import "../tasks/tasks_intrahost.wdl" as intrahost -workflow sarscov2_nextstrain_noSub { +workflow sarscov2_nextstrain { meta { - description: "Align assemblies, build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/" - author: "Broad Viral Genomics" - email: "viral-ngs@broadinstitute.org" + description: "Modified version of the Broad's sars_cov2_nextstrain WDL Worfklow to align assemblies, build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/" + author: "Kevin Libuit" + email: "kevin.libuit@theiagen.com" } input { diff --git a/workflows/wf_titan_augur_run.wdl b/workflows/wf_titan_augur_run.wdl index 4e71f883..415d54e2 100644 --- a/workflows/wf_titan_augur_run.wdl +++ b/workflows/wf_titan_augur_run.wdl @@ -1,13 +1,13 @@ version 1.0 -import "wf_sarscov2_nextstrain_noSub.wdl" as augur_noSub +import "wf_sarscov2_nextstrain_modified.wdl" as augur import "../tasks/task_phylo.wdl" as phylo import "../tasks/task_data_vis.wdl" as vis workflow titan_augur_run { meta { - description: "Meant for SC2 cluster investigations. Titan_Augur_Run will run Augur without a subsampling module using a modified version of the Braod's sarscov2_nextstrain WDL workflow to create an Auspice JSON file; output from the modified sarscov2_nextstrain workflow will also be used to infer SNP distances and create a static PDF report" - author: "Broad Viral Genomics" + description: "Workflow for SC2 cluster investigations. Titan_Augur_Run will run Augur without a subsampling module using a modified version of the Braod's sarscov2_nextstrain WDL workflow to create an Auspice JSON file; output from the modified sarscov2_nextstrain workflow will also be used to infer SNP distances and create a static PDF report" + author: "Kevin G Libuit" email: "kevin.libuit@theiagen.com" } @@ -29,7 +29,7 @@ workflow titan_augur_run { } } - call augur_noSub.sarscov2_nextstrain_noSub { + call augur.sarscov2_nextstrain { input: assembly_fastas=assembly_fastas, sample_metadata_tsvs=sample_metadata_tsvs, @@ -39,25 +39,25 @@ workflow titan_augur_run { call phylo.snp_dists { input: cluster_name = build_name, - alignment = sarscov2_nextstrain_noSub.mafft_alignment + alignment = sarscov2_nextstrain.mafft_alignment } call vis.cluster_render { input: cluster_name = build_name, snp_matrix = snp_dists.snp_matrix, - ml_tree = sarscov2_nextstrain_noSub.ml_tree, + ml_tree = sarscov2_nextstrain.ml_tree, } output { - File combined_assemblies = sarscov2_nextstrain_noSub.combined_assemblies - File MAFFT_alignment = sarscov2_nextstrain_noSub.mafft_alignment - File unmasked_snps = sarscov2_nextstrain_noSub.unmasked_snps + File combined_assemblies = sarscov2_nextstrain.combined_assemblies + File MAFFT_alignment = sarscov2_nextstrain.mafft_alignment + File unmasked_snps = sarscov2_nextstrain.unmasked_snps - File metadata_merged = sarscov2_nextstrain_noSub.metadata_merged - File keep_list = sarscov2_nextstrain_noSub.keep_list - File time_tree = sarscov2_nextstrain_noSub.time_tree + File metadata_merged = sarscov2_nextstrain.metadata_merged + File keep_list = sarscov2_nextstrain.keep_list + File time_tree = sarscov2_nextstrain.time_tree - File auspice_input_json = sarscov2_nextstrain_noSub.auspice_input_json + File auspice_input_json = sarscov2_nextstrain.auspice_input_json File analysis_doc = cluster_render.analysis_doc File snp_list = cluster_render.snp_list File snp_matrix = snp_dists.snp_matrix