From 47ffae2b0805854e3421930f95efcba054d286e9 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Fri, 8 Dec 2023 11:50:24 +0000 Subject: [PATCH 1/2] update README --- README.md | 6 +++--- dxapp.json | 9 ++++++--- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 6ef0d95..6e6cf2f 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,16 @@ -dnanexus_normals_readcount_analysis_v1.0.0 +dnanexus_normals_readcount_analysis_v1.1.0 Exome depth is run in two stages. Firstly, read counts are calculated and the second step filers out the CNVs of interest. Read counts are calculated over the entire genome and the CNVs are filtered out using a subpanel BED file. CNV calling can be performed by providing a readcount file for a set of known normals. -dnanexus_normals_readcount_analysis_v1.0.0 calculates readcounts for a panel of normals samples intended to use as an input for https://github.com/moka-guys/dnanexus_ED_readcount_analysis +dnanexus_normals_readcount_analysis_v1.1.0 calculates readcounts for a panel of normals samples intended to use as an input for https://github.com/moka-guys/dnanexus_ED_readcount_analysis What does the app do? This app runs the read count calculation stage for a set of known normals. Using the provided DNANexus project and the list of Pan numbers the app downloads BAMs and BAI. -A Docker image containing Exome depth is downloaded from 001 - The Exomedepth image taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.0.0 +A Docker image containing Exome depth is downloaded from 001 - The Exomedepth image taken from https://github.com/moka-guys/seglh-cnv/releases/tag/v2.1.0 The readCount.R script is then called, producing a readcount file (normals.RData) diff --git a/dxapp.json b/dxapp.json index 3bd6496..2652684 100644 --- a/dxapp.json +++ b/dxapp.json @@ -1,8 +1,11 @@ { - "name": "ED_panel_of_normals_v1.0.0", - "title": "ED_panel_of_normals_v1.0.0", - "summary": "v1.0.0 - Create panel of normals for cnv calling", + "name": "ED_panel_of_normals_v1.1.0", + "title": "ED_panel_of_normals_v1.1.0", + "summary": "v1.1.0 - Create panel of normals for cnv calling", "dxapi": "1.0.0", + "properties": { + "github release": "v1.1.0" + }, "inputSpec": [ { "name": "project_name", From 1aea237e4111ff034d752740129f28de1c5e4719 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Fri, 8 Dec 2023 11:54:15 +0000 Subject: [PATCH 2/2] update image id in code --- src/code.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/code.sh b/src/code.sh index 6d08a59..0ad3f5b 100644 --- a/src/code.sh +++ b/src/code.sh @@ -1,5 +1,5 @@ #!/bin/bash -# ED_panel_of_normals_v1.0.0 +# ED_panel_of_normals_v1.1.0 # The following line causes bash to exit at any point if there is any error # and to output each line as it is executed -- useful for debugging @@ -74,7 +74,7 @@ cd /home/dnanexus mark-section "setting up Exomedepth docker image" # Location of the ExomeDepth docker file -docker_file_id=project-ByfFPz00jy1fk6PjpZ95F27J:file-GYzKz400jy1yx101F34p8qj2 +docker_file_id=project-ByfFPz00jy1fk6PjpZ95F27J:file-Gbjy9yj0JQXkKB8bfFz856V6 # download the docker file from 001_Tools... dx download $docker_file_id --auth "${API_KEY}" docker_file=$(dx describe ${docker_file_id} --name)