diff --git a/README.md b/README.md index f0b5d6b..705792e 100644 --- a/README.md +++ b/README.md @@ -23,23 +23,21 @@ nextflow run main.nf --pipeline toxin --project /debug/20220501_ ``` ## cellprofiler-nf help -```ruby -log.info ''' +``` C E L L P R O F I L E R - N F P I P E L I N E =============================================== -''' - log.info "Usage:" - log.info "The typical command for running the pipeline is as follows:" - log.info "nextflow run main.nf --pipeline --project " - log.info "" - log.info "Mandatory arguments:" - log.info "--project The path to your project directory" - log.info "--pipeline The CP pipeline to use: toxin, dauer" - log.info "" - log.info "Optional arguments:" - log.info "--groups comma separated metadata groupings for CellProfiler, default is plate,well" - log.info "--outdir Output directory to place files, default is project/Analysis-{current date}" - log.info "--help This usage statement." +Usage: +The typical command for running the pipeline is as follows: +nextflow run main.nf --pipeline --project + +Mandatory arguments: +--project The path to your project directory +--pipeline The CP pipeline to use: toxin, dauer + +Optional arguments: +--groups comma separated metadata groupings for CellProfiler, default is plate,well +--outdir Output directory to place files, default is project/Analysis-{current date} +--help This usage statement. ``` ## Input directory structure diff --git a/img/cellprofiler-nf_workflow.png b/img/cellprofiler-nf_workflow.png deleted file mode 100644 index 3a649c8..0000000 Binary files a/img/cellprofiler-nf_workflow.png and /dev/null differ diff --git a/img/cellprofiler-nf_workflow.svg b/img/cellprofiler-nf_workflow.svg deleted file mode 100644 index c488823..0000000 --- a/img/cellprofiler-nf_workflow.svg +++ /dev/null @@ -1,4 +0,0 @@ - - - -
Project
Folder
Project...
Configure CP input
Configure CP input
Run CP
Run CP
Process CP output
Process CP output
.../{ProjectFolder}/Analysis-{date}processed_images
{proc_image_names}.png
{proc_image_names}.png
processed_data
{proj}_Analysis-{date}.RData
{proj}_Analysis-{date}.RDa...
{model_names}.csv
{model_names}.csv
.../{ProjectFolder}/Analysis-{date}metadata
metadata.csv
metadata.csv
pipeline
pipeline.cppipe
pipeline.cppipe
groups
groups.csv
groups.csv
Text is not SVG - cannot display
\ No newline at end of file