From b050268db8fc1817995e7179193bd59394dee294 Mon Sep 17 00:00:00 2001 From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com> Date: Thu, 7 Sep 2023 17:01:53 -0400 Subject: [PATCH] add info on looper report and point to pepatac example https://github.com/pepkit/looper/issues/41 --- docs/features.md | 1 + docs/looper-report.md | 11 ++++++++++ docs/usage.md | 50 ++++++------------------------------------- mkdocs.yml | 1 + 4 files changed, 20 insertions(+), 43 deletions(-) create mode 100644 docs/looper-report.md diff --git a/docs/features.md b/docs/features.md index f31e79c26..c45ff71f9 100644 --- a/docs/features.md +++ b/docs/features.md @@ -46,3 +46,4 @@ Looper uses a command-line interface so you have total power at your fingertips. ![html][html] **Beautiful linked result reports** Looper automatically creates an internally linked, portable HTML report highlighting all results for your pipeline, for every pipeline. +For an html report example see: [PEPATAC Gold Summary](https://pepatac.databio.org/en/latest/files/examples/gold/gold_summary.html) \ No newline at end of file diff --git a/docs/looper-report.md b/docs/looper-report.md new file mode 100644 index 000000000..c98f5aa8c --- /dev/null +++ b/docs/looper-report.md @@ -0,0 +1,11 @@ +# Create a Browsable HTML Report + +Looper can create a browsable html report of all project results using the command: + +```terminal +looper report --looper-config .your_looper_config.yaml +``` + +An example html report out put can be found here: [PEPATAC Gold Summary](https://pepatac.databio.org/en/latest/files/examples/gold/gold_summary.html) + +Note: pipestat must be configured by looper to perform this operation. Please see the pipestat section for more information: [Using pipestat](pipestat.md) \ No newline at end of file diff --git a/docs/usage.md b/docs/usage.md index dd9812e1a..2cd6e60b7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -26,7 +26,7 @@ Each task is controlled by one of the following commands: `run`, `rerun`, `runp` Here you can see the command-line usage instructions for the main looper command and for each subcommand: ## `looper --help` ```console -version: 1.5.0 +version: 1.5.2-dev usage: looper [-h] [--version] [--logfile LOGFILE] [--dbg] [--silent] [--verbosity V] [--logdev] {run,rerun,runp,table,report,destroy,check,clean,inspect,init,init-piface} @@ -45,7 +45,7 @@ positional arguments: check Check flag status of current runs. clean Run clean scripts of already processed jobs. inspect Print information about a project. - init Initialize looper dotfile. + init Initialize looper config file. init-piface Initialize generic pipeline interface. options: @@ -64,9 +64,7 @@ https://github.com/pepkit/looper ## `looper run --help` ```console usage: looper run [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S] - [-c K [K ...]] [-u X] [-n N] [--looper-config LOOPER_CONFIG] - [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] @@ -88,9 +86,7 @@ options: -f, --skip-file-checks Do not perform input file checks -u X, --lump X Total input file size (GB) to batch into one job -n N, --lumpn N Number of commands to batch into one job - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -119,9 +115,7 @@ sample selection arguments: ## `looper runp --help` ```console usage: looper runp [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] [-s S] - [-c K [K ...]] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] - [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [config_file] @@ -140,10 +134,7 @@ options: -x S, --command-extra S String to append to every command -y S, --command-extra-override S Same as command-extra, but overrides values in PEP -f, --skip-file-checks Do not perform input file checks - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -172,9 +163,7 @@ sample selection arguments: ## `looper rerun --help` ```console usage: looper rerun [-h] [-i] [-d] [-t S] [-x S] [-y S] [-f] [--divvy DIVCFG] [-p P] - [-s S] [-c K [K ...]] [-u X] [-n N] [--looper-config LOOPER_CONFIG] - [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] @@ -196,9 +185,7 @@ options: -f, --skip-file-checks Do not perform input file checks -u X, --lump X Total input file size (GB) to batch into one job -n N, --lumpn N Number of commands to batch into one job - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -226,9 +213,7 @@ sample selection arguments: ## `looper report --help` ```console - usage: looper report [-h] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] - [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [--project] [config_file] @@ -241,9 +226,7 @@ positional arguments: options: -h, --help show this help message and exit - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -263,9 +246,7 @@ sample selection arguments: ## `looper table --help` ```console - usage: looper table [-h] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] - [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [--project] [config_file] @@ -278,9 +259,7 @@ positional arguments: options: -h, --help show this help message and exit - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -300,9 +279,7 @@ sample selection arguments: ## `looper inspect --help` ```console - usage: looper inspect [-h] [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] - [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [--sample-names [SAMPLE_NAMES ...]] [--attr-limit ATTR_LIMIT] @@ -316,9 +293,7 @@ positional arguments: options: -h, --help show this help message and exit - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -340,12 +315,12 @@ sample selection arguments: ## `looper init --help` ```console usage: looper init [-h] [-f] [-o DIR] [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-p] - config_file + pep_config -Initialize looper dotfile. +Initialize looper config file. positional arguments: - config_file Project configuration file (YAML) + pep_config Project configuration file (PEP) options: -h, --help show this help message and exit @@ -360,12 +335,10 @@ options: ## `looper destroy --help` ```console - usage: looper destroy [-h] [-d] [--force-yes] [--looper-config LOOPER_CONFIG] - [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] - [-a A [A ...]] + [-a A [A ...]] [--project] [config_file] Remove output files of the project. @@ -379,14 +352,13 @@ options: -d, --dry-run Don't actually submit the jobs. Default=False --force-yes Provide upfront confirmation of destruction intent, to skip console query. Default=False - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] Path to looper project config file -a A [A ...], --amend A [A ...] List of amendments to activate + --project Process project-level pipelines sample selection arguments: Specify samples to include or exclude based on sample attribute values @@ -401,9 +373,7 @@ sample selection arguments: ## `looper check --help` ```console usage: looper check [-h] [--describe-codes] [--itemized] [-f [F ...]] - [--looper-config LOOPER_CONFIG] [-S YAML [YAML ...]] - [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] [--project] [config_file] @@ -419,9 +389,7 @@ options: --describe-codes Show status codes description --itemized Show a detailed, by sample statuses -f [F ...], --flags [F ...] Check on only these flags/status values - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] @@ -441,9 +409,7 @@ sample selection arguments: ## `looper clean --help` ```console - usage: looper clean [-h] [-d] [--force-yes] [--looper-config LOOPER_CONFIG] - [-S YAML [YAML ...]] [-P YAML [YAML ...]] [-l N] [-k N] [--sel-attr ATTR] [--sel-excl [E ...] | --sel-incl [I ...]] [-a A [A ...]] @@ -460,9 +426,7 @@ options: -d, --dry-run Don't actually submit the jobs. Default=False --force-yes Provide upfront confirmation of destruction intent, to skip console query. Default=False - --looper-config LOOPER_CONFIG Looper configuration file (YAML) - -S YAML [YAML ...], --sample-pipeline-interfaces YAML [YAML ...] Path to looper sample config file -P YAML [YAML ...], --project-pipeline-interfaces YAML [YAML ...] diff --git a/mkdocs.yml b/mkdocs.yml index 42e754f46..8330b53e7 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -24,6 +24,7 @@ nav: - Writing a pipeline interface: writing-a-pipeline-interface.md - Using looper config: looper-config.md - Using geofetch: using-geofetch.md + - Browsable HTML Reports: looper-report.md - Using divvy: - Introduction: divvy/README.md - Configuring divvy: divvy/configuration.md