From 89f22987534ea8fdd28ff19b88cff8a9d6fdc91f Mon Sep 17 00:00:00 2001 From: Nana Mensah Date: Thu, 9 Apr 2020 09:02:31 +0100 Subject: [PATCH 1/3] Update v1.8 README --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 9a575ce..5329d94 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# Workstation Housekeeping v1.7 +# Workstation Housekeeping v1.8 Scripts to manage data on the NGS workstation @@ -62,7 +62,6 @@ wscleaner --version # Print version number ### Usage ```bash -wscleaner --set-key DNA_NEXUS_KEY # Cache dnanexus api key wscleaner ROOT_DIRECTORY --logfile LOGFILE_PATH ``` From 7be72f999bfa21e121d635e02335d513bfc0df17 Mon Sep 17 00:00:00 2001 From: Nana Mensah Date: Thu, 9 Apr 2020 09:03:04 +0100 Subject: [PATCH 2/3] Update DESIGN.md --- wscleaner/DESIGN.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wscleaner/DESIGN.md b/wscleaner/DESIGN.md index 8259925..676c413 100644 --- a/wscleaner/DESIGN.md +++ b/wscleaner/DESIGN.md @@ -29,4 +29,4 @@ NF4. Attempt to process all folders at least once A RunFolderManager class will instatiate objects for local Runfolders, each of which has an associated DNA Nexus project object. The manager loops over the runfolders and deletes them if all checks pass. -DNA Nexus projects are accessed with the dxpy module, a python wrapper for the DNA Nexus API. Credentials are cached locally using the command-line option '--set-key'. +DNA Nexus projects are accessed with the dxpy module, a python wrapper for the DNA Nexus API. From a92ac465d85ff72e7558539348e50c71211dcc1d Mon Sep 17 00:00:00 2001 From: Nana Mensah Date: Thu, 9 Apr 2020 09:06:54 +0100 Subject: [PATCH 3/3] Update README.md --- wscleaner/README.md | 27 +++++++++++++++------------ 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/wscleaner/README.md b/wscleaner/README.md index 91c17fb..a19d3af 100644 --- a/wscleaner/README.md +++ b/wscleaner/README.md @@ -21,28 +21,31 @@ wscleaner --version # Print version number ## Quickstart ```bash -wscleaner --set-key DNA_NEXUS_KEY # Cache dnanexus api key wscleaner ROOT_DIRECTORY ``` ## Usage ``` -wscleaner [-h] [--set-key SET_KEY] [--print-key] [--dry-run] - [--logfile LOGFILE] [--min-age MIN_AGE] [--version] - root +usage: wscleaner [-h] [--auth AUTH] [--dry-run] [--logfile LOGFILE] + [--min-age MIN_AGE] [--logfile-count LOGFILE_COUNT] + [--version] + root positional arguments: - root A directory containing runfolders to process + root A directory containing runfolders to process optional arguments: - -h, --help show this help message and exit - --set-key SET_KEY Cache a DNA Nexus API key - --print-key Print the cached DNA Nexus API key - --dry-run Perform a dry run without deleting files - --logfile LOGFILE A path for the application logfile - --min-age MIN_AGE The age (days) a runfolder must be to be deleted - --version Print version + -h, --help show this help message and exit + --auth AUTH A text file containing the DNANexus authentication + token + --dry-run Perform a dry run without deleting files + --logfile LOGFILE A path for the application logfile + --min-age MIN_AGE The age (days) a runfolder must be to be deleted + --logfile-count LOGFILE_COUNT + The number of logfiles a runfolder must have in + /Logfiles + --version Print version ``` ## Test