Commit 73bb7394 authored by mmassaviol's avatar mmassaviol
Browse files

Add general params section

parent 3ed871ab
App:
project: /home/mbb/Documents/sag/app2
general: { title: Pipeline in R, skin: purple, menu_width: 230 }
general: {title: RNAseq pipeline, skin: blue, menu_width: 230}
pages:
- icon: pencil
label: Quality check
name: qualitycheck
content:
- panel: Quality check
name: panel1
boxes:
- { name: fastqc, defined: true, concat_name_param: false }
pipeline:
shiny_button:
{
name: runP,
type: button,
icon: save,
class: btn btn-primary,
label: Run pipeline,
}
program: python
options:
- {
name: "",
type: value,
value: /home/jimmy/jimmy/projets/sag/app/mon_script.py,
}
- { name: -params_file, type: panel }
output_format: markdown
output: /home/jimmy/jimmy/projets/sag/app/result.Rmd
- name: quantification
icon: file
label: Quantification
content:
- panel: Quantification
name: panel2
boxes:
- { name: kallisto, defined: true, concat_name_param: false }
- { name: salmon, defined: true, concat_name_param: false }
pipeline:
shiny_button:
{
name: runApp,
type: button,
icon: play,
class: btn btn-primary,
label: Run,
}
program: pwd
options:
- { name: "", type: shiny, value: first_name }
- { name: "", type: shiny, value: last_name }
output_format: table
output: /home/jimmy/jimmy/projets/sag/app/cars.csv
- icon: pencil
label: Global parameters
name: global_params
content:
- panel: Global parameters
name: global_params
boxes:
- name: global_params
title: 'Global parameters :'
status: success
defined: false
content:
- {name: sample_directory, type: text, value: /, label: 'Samples directory: '}
- {name: sample_suffix, type: text, value: .fastq.gz, label: 'Samples suffix: '}
- {name: transcripts_adress, type: text, value: transcripts.fasta.gz, label: 'Transcripts address: '}
- {name: genome_adress, type: text, value: genome.fasta.gz, label: 'Genome address: '}
- {name: annotations_adress, type: text, value: annotations.gtf.gz, label: 'Annotations address: '}
pipeline:
shiny_button: {name: runP, type: button, icon: save, class: btn btn-primary, label: Run pipeline}
program: python
options:
- {name: null, type: value, value: /home/jimmy/jimmy/projets/sag/app/mon_script.py}
- {name: -params_file, type: panel}
output_format: markdown
output: /home/jimmy/jimmy/projets/sag/app/result.Rmd
- icon: pencil
label: Quality check
name: quality_check
content:
- panel: Quality check
name: quality_check
boxes:
- {name: fastqc, defined: true, concat_name_param: false}
pipeline:
shiny_button: {name: runP, type: button, icon: save, class: btn btn-primary,
label: Run pipeline}
program: python
options:
- {name: null, type: value, value: /home/jimmy/jimmy/projets/sag/app/mon_script.py}
- {name: -params_file, type: panel}
output_format: markdown
output: /home/jimmy/jimmy/projets/sag/app/result.Rmd
- icon: pencil
label: Quantification
name: quantification
content:
- panel: Quantification
name: quantification
boxes:
- {name: kallisto, defined: true, concat_name_param: false}
- {name: salmon, defined: true, concat_name_param: false}
pipeline:
shiny_button: {name: runP, type: button, icon: save, class: btn btn-primary, label: Run pipeline}
program: python
options:
- {name: null, type: value, value: /home/jimmy/jimmy/projets/sag/app/mon_script.py}
- {name: -params_file, type: panel}
output_format: markdown
output: /home/jimmy/jimmy/projets/sag/app/result.Rmd
pipeline:
shiny_button:
{
name: runAllPipeline,
type: button,
icon: play,
class: btn btn-info,
label: Run pipeline,
}
program: "singularity exec /home/mbb/Documents/singularities/pipelineRNA.simg snakemake"
shiny_button: {name: runAllPipeline, type: button, icon: save, class: btn btn-info, label: Export pipeline}
program: python
options:
- { name: "-s", type: value, value: "snakefile" }
output_format: markdown
output: /home/jimmy/jimmy/projets/sag/app/result.Rmd
- {name: '', type: value, value: make_snakefile.py}
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