"&& index-summary {params.analysis_dir} | sed 's/ \{{2,\}}/,/g' | sed 's/ CV/,CV/' | sed 's/^ //g' | sed 's/,$//g' > index_summary.csv " # format as a csv for multiqc
head = """# description: 'This is the list of the parameters for each rule'
# section_name: 'Workflow parameters'
"""
for step in STEPS:
tool = config[step["name"]]
for key, value in config.items():
if (tool in key and tool != "null") or (key in ["results_dir","sample_dir","sample_suffix","SeOrPe"]) and ((config["SeOrPe"] == "SE" and not("_PE" in command)) or (config["SeOrPe"] == "PE" and not("_SE" in command))):
if (key in PARAMS_INFO.keys() and "label" in PARAMS_INFO[key].keys()):
To run the UI app you should bind data and results directories like in the following example.
You must also provide the host address and port where the shiny app will be launched
exemple : singularity run --app UI -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif 127.0.0.1 1234
%apprun Snakemake
configfile=$1
cores=$2
shift
shift
exec snakemake -s /workflow/Snakefile all --configfile $configfile --cores $cores $@
%apphelp Snakemake
To run the Snakemake app you should bind data and results directories like in the following example.
You must also provide the configfile and the number of cores provided to snakemake command (you can add other parameters after these two)
exemple : singularity run --app Snakemake -B /path/to/data/directory:/Data -B /path/to/store/Results:/Results this_container.sif myconfig.yml 16 otherparams
%apprun getConfigfile
exec cp /workflow/params.total.yml ./params.yml
%apphelp getConfigfile
To run the getConfigfile app you dont need to bind directories. This app will only copy the default parameters file from the container to your local disk.
exemple : singularity run --app getConfigfile this_container.sif
%apprun getSamples
exec python3 /workflow/get_samples.py $1 $2
%apphelp getSamples
To run the getSamples app you need to bind the data directory. This app will give you the list of samples detected in a given directory and their file suffix.
exemple : singularity run --app getSamples -B /path/to/data/directory:/Data this_container.sif /Data PE
%help
This container contains four apps (UI, Snakemake, getConfigfile and getSamples).
* UI is a user interface to set up the workflow and launch it.
* Snakemake let you provide your configfile and other parameters to the snakemake command and launch it.
* getConfigfile gives you a copy of a default parameters file to fill and use with the Snakemake app.
* getSamples gives you the list of samples detected in a given directory and their file suffix (usefull for filling samples and sample_suffix in parameters file).
selectInput("force_from",label="Start again from a step : ",selected="none",choices=list('none'='none','Interop read metrics'='interop_read_metrics',"All"="all")),tags$br(),
tabRUN=fluidPage(box(title='Run :',width=12,status='primary',collapsible=TRUE,solidHeader=TRUE,uiOutput('run_out',style='overflow-y: scroll; height: 600px')),actionButton("unlock","Unlock the directory in case of previous failure"))
