From b19ed0f536cea9817f470f9015e1134f4420810a Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:26:05 -0500 Subject: [PATCH 1/7] remove output no longer generated by general viz script --- pipes/WDL/workflows/create_enterics_qc_viz.wdl | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pipes/WDL/workflows/create_enterics_qc_viz.wdl b/pipes/WDL/workflows/create_enterics_qc_viz.wdl index b9750e5e9..c3cf798de 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz.wdl @@ -34,7 +34,6 @@ workflow CreateEntericsWCViz { output { File viz_pdf = create_viz.vizualizations - File color_chart = create_viz.color_chart } } @@ -48,7 +47,7 @@ task create_viz { String grouping_column_name = "gambit_predicted_taxon" String output_filename = "QC_vizualizations.pdf" - String docker = "broadinstitute/horsefish:pgs_visualizations" + String docker = "broadinstitute/horsefish:pgs_visualizations_dev" } command { @@ -66,6 +65,5 @@ task create_viz { output { File vizualizations = "~{output_filename}" - File color_chart = "Colorized_Scores.xlsx" } } \ No newline at end of file From fadc39ea19062f04d4cd4eef122c1e5c884321b6 Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:32:29 -0500 Subject: [PATCH 2/7] fix spelling of workflow name from WC to QC --- pipes/WDL/workflows/create_enterics_qc_viz.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/create_enterics_qc_viz.wdl b/pipes/WDL/workflows/create_enterics_qc_viz.wdl index c3cf798de..c597bbffa 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz.wdl @@ -1,6 +1,6 @@ version 1.0 -workflow CreateEntericsWCViz { +workflow CreateEntericsQCViz { parameter_meta { sample_ids: {description: "selected rows of data from data table which will be used for plotting"} From a2844cda626593a0b5ed213a69d00d3149e26730 Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:34:17 -0500 Subject: [PATCH 3/7] revert changes to the non-specific version of QC viz --- pipes/WDL/workflows/create_enterics_qc_viz.wdl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/create_enterics_qc_viz.wdl b/pipes/WDL/workflows/create_enterics_qc_viz.wdl index c597bbffa..a5a9b53ac 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz.wdl @@ -34,6 +34,7 @@ workflow CreateEntericsQCViz { output { File viz_pdf = create_viz.vizualizations + File color_chart = create_viz.color_chart } } @@ -47,7 +48,7 @@ task create_viz { String grouping_column_name = "gambit_predicted_taxon" String output_filename = "QC_vizualizations.pdf" - String docker = "broadinstitute/horsefish:pgs_visualizations_dev" + String docker = "broadinstitute/horsefish:pgs_visualizations" } command { @@ -65,5 +66,6 @@ task create_viz { output { File vizualizations = "~{output_filename}" + File color_chart = "Colorized_Scores.xlsx" } } \ No newline at end of file From d5fef8bba00f0df5d69c30d241b33268fecfbeea Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:36:06 -0500 Subject: [PATCH 4/7] create general WDL version of enterics --- .../create_enterics_qc_viz_general.wdl | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 pipes/WDL/workflows/create_enterics_qc_viz_general.wdl diff --git a/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl new file mode 100644 index 000000000..93cf22f0c --- /dev/null +++ b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl @@ -0,0 +1,69 @@ +version 1.0 + +workflow CreateEntericsQCVizGeneral { + + parameter_meta { + sample_ids: {description: "selected rows of data from data table which will be used for plotting"} + input_table_name: {description: "name of the Terra data table - root entity type - from where input data is selected"} + workspace_name: {description: "name of Terra workspace where data lives"} + workspace_project: {description: "name of Terra project associated with Terra workspace"} + grouping_column_name: {description: "name of column to be used for grouping/coloring - ex. gambit_predicted_taxon (organism)"} + output_filename: {description: "name of output file containing visualizations"} + } + + input { + + Array[String] sample_ids + String input_table_name + String workspace_name + String workspace_project + + String? grouping_column_name + String? output_filename + } + + call create_viz { + input: + sample_ids = sample_ids, + workspace_name = workspace_name, + workspace_project = workspace_project, + input_table_name = input_table_name, + grouping_column_name = grouping_column_name, + output_filename = output_filename + } + + output { + File viz_pdf = create_viz.vizualizations + } +} + +task create_viz { + input { + Array[String] sample_ids + String workspace_name + String workspace_project + String input_table_name + + String grouping_column_name = "gambit_predicted_taxon" + String output_filename = "QC_vizualizations.pdf" + + String docker = "broadinstitute/horsefish:pgs_visualizations_dev" + } + + command { + python3 /scripts/create_visualizations.py -s ~{sep=' ' sample_ids} \ + -t ~{input_table_name} \ + -w ~{workspace_name} \ + -p ~{workspace_project} \ + ~{"-g" + grouping_column_name} \ + ~{"-o" + output_filename} + } + + runtime { + docker: docker + } + + output { + File vizualizations = "~{output_filename}" + } +} \ No newline at end of file From 588f771deb253337a24a7d445ec7440f512e8794 Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:37:34 -0500 Subject: [PATCH 5/7] add general version to dockstore yaml " --- .dockstore.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.dockstore.yml b/.dockstore.yml index d1892afca..5b969eb03 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -380,3 +380,9 @@ workflows: primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz.wdl testParameterFiles: - empty.json + + - name: create_enterics_qc_viz_general + subclass: WDL + primaryDescriptorPath: /pipes/WDL/workflows/create_enterics_qc_viz_general.wdl + testParameterFiles: + - empty.json From 3dad64c9412ebed8dec80dce45dbd2616aef29e4 Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Thu, 14 Dec 2023 17:56:18 -0500 Subject: [PATCH 6/7] change nmae of python script in command block --- pipes/WDL/workflows/create_enterics_qc_viz_general.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl index 93cf22f0c..9843ea897 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl @@ -51,7 +51,7 @@ task create_viz { } command { - python3 /scripts/create_visualizations.py -s ~{sep=' ' sample_ids} \ + python3 /scripts/general_create_visualizations.py -s ~{sep=' ' sample_ids} \ -t ~{input_table_name} \ -w ~{workspace_name} \ -p ~{workspace_project} \ From e792b241bcfa974ecdcc361ca1403050f8dc7599 Mon Sep 17 00:00:00 2001 From: Sushma Chaluvadi Date: Fri, 15 Dec 2023 12:25:57 -0500 Subject: [PATCH 7/7] swap from dev docker image --- pipes/WDL/workflows/create_enterics_qc_viz_general.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl index 9843ea897..ecf0531f8 100644 --- a/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl +++ b/pipes/WDL/workflows/create_enterics_qc_viz_general.wdl @@ -47,7 +47,7 @@ task create_viz { String grouping_column_name = "gambit_predicted_taxon" String output_filename = "QC_vizualizations.pdf" - String docker = "broadinstitute/horsefish:pgs_visualizations_dev" + String docker = "broadinstitute/horsefish:pgs_visualizations" } command {