Commit 10455e1a authored by mmassaviol's avatar mmassaviol
Browse files

Big update

parent 73bb7394
This diff is collapsed.
App:
project: /home/mbb/Documents/sag/app2
general: {title: RNAseq pipeline, skin: blue, menu_width: 230}
pages:
- icon: pencil
label: 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: '}
- icon: pencil
label: Quality check
name: quality_check
boxes:
- {name: fastqc, defined: true, concat_name_param: false}
- icon: pencil
label: Quantification
name: quantification
boxes:
- {name: kallisto, defined: true, concat_name_param: false}
- {name: salmon, defined: true, concat_name_param: false}
run:
shiny_button: {name: RunPipeline, type: button, icon: pencil, class: btn btn-info, label: Run pipeline}
program: snakemake
options:
- {name: '-v', type: value, value: ""}
download:
shiny_button: {name: DownloadPipeline, type: button, class: btn btn-light, label: Download pipeline}
......@@ -3,6 +3,6 @@ name: "fastqc",
title: "FastQC :",
status: "success",
content: [
{name: "threads_fastqc", type: "slider", min: 1, max: 16, step: 1, value: [1], label: "Number of threads to use :"},
{name: "fastqc_threads", type: "slider", min: 1, max: 16, step: 1, value: [1], label: "Number of threads to use :"},
]
}
......@@ -3,8 +3,9 @@ name: "kallisto",
title: "kallisto :",
status: "success",
content: [
{name: "kallisto_index_input", type: "file", multiple: FALSE, accept: [".fasta", ".fasta.gz"], label: "Choose reference fasta file :"},
{name: "kallisto_index_input", type: "file", multiple: FALSE, accept: [".fasta", ".fasta.gz"], label: "Choose reference fasta file: "},
{name: "help_strand", type: "help", label: "For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse"},
{name: "kallisto_quant_pe_stranded", type: "radio", selected: "No", choices: ["No", "--fr-stranded", "--rf-stranded"], label: "Strand specific mode :"},
{name: "kallisto_quant_pe_stranded", type: "radio", selected: "No", choices: ["No", "--fr-stranded", "--rf-stranded"], label: "Strand specific mode: "},
{name: "kallisto_quant_threads", type: "slider", min: 1, max: 16, step: 1, value: [1], label: "Number of threads to use: "},
]
}
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