Update, default tool selection and group loading with sample detection

main.R

@@ -123,7 +123,7 @@ generate_page_input <- function(res, cnt) {
       }
     }
     
-    res <- res + ' selected = "'+cnt$selected+'"' + ', width =  "'+ 'auto' +'")'
+    res <- res + ' selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
     
   } else if(cnt$type == "radio") {
     
@@ -142,7 +142,7 @@ generate_page_input <- function(res, cnt) {
       }
     }
     
-    res <- res + ' selected = "'+cnt$selected+'"' + ', width =  "'+ 'auto' +'")'
+    res <- res + ' selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
     
   } else if(cnt$type == "checkbox") {
     
@@ -201,7 +201,7 @@ generate_page_input <- function(res, cnt) {
       }
     }
     
-    res <- res + '), selected = "'+cnt$selected+'"' + ', width =  "'+ 'auto' +'")'
+    res <- res + '), selected = "'+cnt$value+'"' + ', width =  "'+ 'auto' +'")'
     
   } else if(cnt$type == "file") {
     
@@ -308,7 +308,7 @@ generate_pages_server <- function() {
       if(length(boxes) > 0) {
         
         if(length(boxes) > 1){
-          res <- res + '\tselectInput("select' + content$name + '", label = "Select the tool to use : ", choices = list(' 
+          res <- res + '\tselectInput("select' + content$name + '", label = "Select the tool to use : ", selected = "' + content$default + '", choices = list(' 
           
           for(b in 1:length(boxes)) { # construction list box tools
             res <- res + '"' + boxes[[b]]$name +'" = "' + boxes[[b]]$name + '"'
@@ -585,6 +585,11 @@ generate_pages_server <- function() {
 	res <- res + '\t\tclass(result) <- "verbatim"\n'
 	res <- res + '\t\treturn(result)\n'
 	res <- res + '\t}\n'
+	
+	res <- res + '\tsamples = yaml.load(system("python3 /workflow/get_samples.py /samples /samples/groups.csv",intern = T))\n'
+	res <- res + '\tc$samples = names(samples)\n'
+	res <- res + '\tc$names(samples) = NULL\n'
+	res <- res + '\tc$groups = unlist(samples)\n'
 	res <- res + '\twrite_yaml(c,"/results/params.yml",handlers=list(logical = logical))\n'
 
 	res <- res + '\ti = sample.int(1000,size = 1)\n'
@@ -616,7 +621,10 @@ generate_pages_server <- function() {
 	res <- res + '\t\tclass(result) <- "verbatim"\n'
 	res <- res + '\t\treturn(result)\n'
 	res <- res + '\t}\n'
-	
+	res <- res + '\tsamples = yaml.load(system("python3 /workflow/get_samples.py /samples /samples/groups.csv",intern = T))\n'
+	res <- res + '\tc$samples = names(samples)\n'
+	res <- res + '\tc$names(samples) = NULL\n'
+	res <- res + '\tc$groups = unlist(samples)\n'
 	res <- res + '\twrite_yaml(c,"/results/params.yml",handlers=list(logical = logical))\n'
 
   res <- res + '\t '
@@ -683,7 +691,7 @@ generate_menu <- function() {
 
   if("DAG" %in% names(APP)){
     name <- "DAG"
-    icon <- "pencil"
+    icon <- "gear"
     menu <- "DAG"
     res <- res + '    menuItem("'+menu+'", tabName="'+name+'", icon=icon("'+icon+'", lib="font-awesome"), newtab=FALSE),\n\n'
   }
@@ -697,13 +705,13 @@ generate_menu <- function() {
   
   res <- res + '    tags$br(),\n\n'
 
-  res <- res + '    numericInput("cores", label = "Threads availaible", min = 1, max = NA, step = 1, width =  "auto", value = 4),\n'
+  res <- res + '    numericInput("cores", label = "Threads available", min = 1, max = NA, step = 1, width =  "auto", value = 4),\n'
 
   if("DAG" %in% names(APP)){
 
     res <- res + '    tags$br(),\n\n'
 
-    res <- res + '    actionButton("DAG", "DAG", icon("pencil") , class="btn btn-info"),\n\n'
+    res <- res + '    actionButton("DAG", "DAG", icon("gear") , class="btn btn-info"),\n\n'
 
   }
 

pipeline.yml

@@ -9,95 +9,195 @@ App:
     - name: global_params
       title: 'Global parameters :'
       status: success
-      defined: false
       content:
-      - {name: sample_dir, type: text, value: /, label: 'Samples directory: '}
+      - {name: sample_dir, type: text, value: /samples, label: 'Samples directory: '}
       - {name: sample_suffix, type: text, value: .fastq.gz, label: 'Samples suffix: '}
-      - {name: results_dir, type: text, value: /home/mbb/Documents/results, label: 'Results
-          directory: '}
+      - {name: results_dir, type: text, value: /results, label: 'Results directory: '}
       - name: SeOrPe
         type: radio
-        selected: PE
+        value: PE
         choices:
         - {Single end: SE}
         - {Paired end: PE}
         label: 'Single end reads (SE) or Paired end reads (PE): '
+  - icon: pencil
+    label: Trimming
+    name: trimming
+    default: 'null'
+    boxes:
+    - name: trimmomatic
+      title: Trimmomatic
+      status: success
+      content:
+      - {name: trimmomatic_threads, prefix: -threads, type: numeric, value: 4, min: 1,
+        max: NA, step: 1, label: Number of threads to use}
+      - name: trimmomatic_qc_score
+        type: radio
+        value: -phred64
+        choices:
+        - {phred33: -phred33}
+        - {phred64: -phred64}
+        label: Quality score encoding
+      - {name: trimmomatic, type: help, label: 'Trimmomatic: A flexible read trimming
+          tool for Illumina NGS data'}
+      - {name: trimmomatic, type: link, label: 'Website : ', href: 'http://www.usadellab.org/cms/?page=trimmomatic'}
+      - {name: trimmomatic, type: link, label: 'Documentation : ', href: 'http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf'}
+      - {name: trimmomatic, type: link, label: 'Paper : ', href: 'https://doi.org/10.1093/bioinformatics/btu170'}
+    - name: 'null'
+      title: 'null'
+      status: success
+      content:
+      - {name: null, type: help, label: 'null: Skip this step'}
   - icon: pencil
     label: Quality check
     name: quality_check
+    default: fastqc
     boxes:
     - name: fastqc
       title: FastQC
       status: success
       content:
-      - {name: fastqc, type: help, label: A quality control tool for high throughput
-          raw sequence data.}
-      - {name: fastqc, type: link, label: 'Website : ', href: 'https://www.bioinformatics.babraham.ac.uk/projects/fastqc/'}
-      - {name: fastqc_threads, prefix: -t, type: numeric, default: 1, min: 1, max: NA,
+      - {name: fastqc_threads, prefix: -t, type: numeric, value: 4, min: 1, max: NA,
         step: 1, label: Number of threads to use}
+      - {name: fastqc, type: help, label: 'FastQC: A quality control tool for high
+          throughput raw sequence data.'}
+      - {name: fastqc, type: link, label: 'Website : ', href: 'https://www.bioinformatics.babraham.ac.uk/projects/fastqc/'}
+      - {name: fastqc, type: link, label: 'Documentation : ', href: 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/'}
   - icon: pencil
     label: Quantification
     name: quantification
+    default: kallisto
     boxes:
     - name: kallisto
       title: kallisto
       status: success
       content:
-      - {name: kallisto, type: help, label: 'kallisto is a program for quantifying
-          abundances of transcripts from RNA-Seq data, or more generally of target
-          sequences using high-throughput sequencing reads.'}
-      - {name: kallisto, type: link, label: 'Website : ', href: 'https://pachterlab.github.io/kallisto/'}
-      - {name: kallisto, type: link, label: 'Paper : ', href: 'https://doi.org/10.1038/nbt.3519'}
-      - {name: kallisto_quant_threads, prefix: -t, type: numeric, default: 1, min: 1,
+      - {name: kallisto_index_input, type: text, value: '', label: Address to reference
+          fasta file}
+      - {name: kallisto_quant_threads, prefix: -t, type: numeric, value: 4, min: 1,
         max: NA, step: 1, label: Number of threads to use}
-      - name: kallisto_quant_pe_stranded
+      - {name: kallisto_quant_SE_fragment_length, prefix: -l, type: numeric, value: 300,
+        min: 1, max: NA, step: 1, label: Estimated average fragment length}
+      - {name: kallisto_quant_SE_standard_deviation, prefix: -s, type: numeric, value: 2,
+        min: 1, max: NA, step: 1, label: Estimated standard deviation of fragment
+          length}
+      - name: kallisto_quant_PE_stranded
         type: radio
         choices:
         - {Not stranded: ''}
         - {Forward Reverse: --fr-stranded}
         - {Reverse Forward: --rf-stranded}
-        default: ''
+        value: ''
         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, type: help, label: 'kallisto: kallisto is a program for quantifying
+          abundances of transcripts from RNA-Seq data, or more generally of target
+          sequences using high-throughput sequencing reads.'}
+      - {name: kallisto, type: link, label: 'Website : ', href: 'https://pachterlab.github.io/kallisto/'}
+      - {name: kallisto, type: link, label: 'Documentation : ', href: 'https://pachterlab.github.io/kallisto/manual'}
+      - {name: kallisto, type: link, label: 'Paper : ', href: 'https://doi.org/10.1038/nbt.3519'}
     - name: salmon
       title: Salmon
       status: success
       content:
-      - {name: salmon, type: help, label: 'Salmon is a tool for quantifying the expression
-          of transcripts using RNA-seq data. '}
-      - {name: salmon, type: link, label: 'Website : ', href: 'https://combine-lab.github.io/salmon/'}
-      - {name: salmon, type: link, label: 'Paper : ', href: 'https://doi.org/10.1038/nmeth.4197'}
-      - {name: salmon_index_threads, prefix: -p, type: numeric, default: 1, min: 1,
+      - {name: salmon_index_input, prefix: -t, type: text, value: '', label: Address
+          to reference fasta file}
+      - {name: salmon_index_threads, prefix: -p, type: numeric, value: 4, min: 1,
         max: NA, step: 1, label: Number of threads to use for index creation}
-      - {name: salmon_quant_threads, prefix: -t, type: numeric, default: 1, min: 1,
+      - {name: salmon_quant_threads, prefix: -t, type: numeric, value: 4, min: 1,
         max: NA, step: 1, label: Number of threads to use}
+      - {name: salmon, type: help, label: 'Salmon: Salmon is a tool for quantifying
+          the expression of transcripts using RNA-seq data. '}
+      - {name: salmon, type: link, label: 'Website : ', href: 'https://combine-lab.github.io/salmon/'}
+      - {name: salmon, type: link, label: 'Documentation : ', href: 'https://salmon.readthedocs.io/en/latest/'}
+      - {name: salmon, type: link, label: 'Paper : ', href: 'https://doi.org/10.1038/nmeth.4197'}
   - icon: pencil
     label: Differential expression
     name: DE
+    default: edger
     boxes:
     - name: edger
       title: edgeR
       status: success
       content:
-      - {name: edger, type: help, label: Empirical Analysis of Digital Gene Expression
-          Data.}
+      - {name: edger_threads, prefix: -t, type: numeric, value: 4, min: 1, max: NA,
+        step: 1, label: Number of threads to use}
+      - {name: edger_tx2gene, type: checkbox, value: false, label: 'Aggregate transcripts
+          counts to gene counts : '}
+      - {name: edger_annotations, type: text, value: '', label: 'Annotation file (gtf
+          or gff) : '}
+      - name: edger_normfact
+        type: radio
+        value: TMM
+        choices:
+        - {TMM: TMM}
+        - {RLE: RLE}
+        - {upperquartile: upperquartile}
+        - {none: none}
+        label: Calculate normalization factors to scale the raw library sizes.
+      - {name: edger_dispersion, type: text, value: '0', label: 'Dispersion: either
+          a numeric vector of dispersions or a character string indicating that dispersions
+          should be taken from the data.'}
+      - name: edger_testType
+        type: radio
+        value: exactTest
+        choices:
+        - {exactTest: exactTest}
+        - {glmLRT: glmLRT}
+        label: 'Test type: exactTest: Computes p-values for differential abundance
+          for each gene between two samples, conditioning on the total count for each
+          gene. The counts in each group are assumed to follow a binomial distribution
+
+          glmLRT: Fits a negative binomial generalized log-linear model to the read
+          counts for each gene and conducts genewise statistical tests.'
+      - {name: edger, type: help, label: 'edgeR: Empirical Analysis of Digital Gene
+          Expression Data.'}
       - {name: edger, type: link, label: 'Website : ', href: 'http://bioconductor.org/packages/release/bioc/html/edgeR.html'}
+      - {name: edger, type: link, label: 'Documentation : ', href: 'http://bioconductor.org/packages/release/bioc/manuals/edgeR/man/edgeR.pdf'}
       - {name: edger, type: link, label: 'Paper : ', href: 'https://doi.org/10.18129/B9.bioc.edgeR'}
     - name: deseq2
       title: DESeq2
       status: success
       content:
-      - {name: deseq2, type: help, label: Differential gene expression analysis based
-          on the negative binomial distribution. Using normalized count data.}
+      - {name: deseq2_threads, prefix: -t, type: numeric, value: 4, min: 1, max: NA,
+        step: 1, label: Number of threads to use}
+      - {name: deseq2_tx2gene, type: checkbox, value: false, label: 'Aggregate transcripts
+          counts to gene counts : '}
+      - {name: deseq2_annotations, type: text, value: '', label: 'Annotation file
+          (gtf or gff) : '}
+      - name: deseq2_fitType
+        type: radio
+        value: parametric
+        choices:
+        - {parametric: parametric}
+        - {local: local}
+        - {mean: mean}
+        label: Type of fitting of dispersions to the mean intensity
+      - {name: deseq2_betaPrior, type: checkbox, value: false, label: 'betaPrior:
+          whether or not to put a zero-mean normal prior on the non-intercept coefficients.
+          By default, the beta prior is used only for the Wald test, but can also
+          be specified for the likelihood ratio test.'}
+      - name: deseq2_testType
+        type: radio
+        value: LRT
+        choices:
+        - {LRT: LRT}
+        - {Wald: Wald}
+        label: 'Test type: Use either Wald significance tests, or the likelihood ratio
+          test on the difference in deviance between a full and reduced model formula'
+      - {name: deseq2, type: help, label: 'DESeq2: Differential gene expression analysis
+          based on the negative binomial distribution. Using normalized count data.'}
       - {name: deseq2, type: link, label: 'Website : ', href: 'https://bioconductor.org/packages/release/bioc/html/DESeq2.html'}
+      - {name: deseq2, type: link, label: 'Documentation : ', href: 'https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf'}
       - {name: deseq2, type: link, label: 'Paper : ', href: 'https://doi.org/10.1186/s13059-014-0550-8'}
   run:
-    shiny_button: {name: RunPipeline, type: button, icon: pencil, class: btn btn-info,
+    shiny_button: {name: RunPipeline, type: button, icon: play, class: btn btn-info,
       label: Run pipeline}
-    program: singularity exec /home/mbb/Documents/singularities/pipelineRNA.simg snakemake
-      -s /home/mbb/Documents/waw/workflows/RNAseq/RNAseq.snakefile --configfile /home/mbb/Documents/test/params/params.yml
+    program: snakemake
     options:
-    - {name: '', type: value, value: ''}
-  download:
-    shiny_button: {name: DownloadPipeline, type: button, class: btn btn-light, label: Download
-        pipeline}
+    - {name: -s, type: value, value: /workflow/Snakefile}
+    - {name: --configfile, type: value, value: /results/params.yml}
+    - {name: -d, type: value, value: /results}
+    - {name: --cores, type: shiny, value: cores}
+  DAG: null
+  Report: null