Feature/DIMS_v3.5_harmonize_NF

DIMS/AssignToBins.nf

@@ -2,18 +2,22 @@ process AssignToBins {
     tag "DIMS AssignToBins ${file_id}"
     label 'AssignToBins'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        tuple(val(file_id), path(mzML_file), path(breaks_file), path(trim_params_file))
+       val(resolution)
 
     output:
        path("${file_id}.RData"), emit: rdata_file
        path("${file_id}_TIC.txt"), emit: tic_txt_file
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/AssignToBins.R $mzML_file $breaks_file $trim_params_file $params.resolution
+        Rscript ${projectDir}/CustomModules/DIMS/AssignToBins.R \
+                $mzML_file \
+                $breaks_file \
+                $trim_params_file \
+                $resolution
         """
 }
 

DIMS/AveragePeaks.R

@@ -11,7 +11,7 @@ preprocessing_scripts_dir <- cmd_args[4]
 tech_reps <- strsplit(techreps, ";")[[1]]
 
 # Load in function scripts
-source(paste0(preprocessing_scripts_dir, "average_peaks_functions.R"))
+source(paste0(preprocessing_scripts_dir, "/average_peaks_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/AveragePeaks.nf

@@ -2,17 +2,21 @@ process AveragePeaks {
     tag "DIMS AveragePeaks"
     label 'AveragePeaks'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(rdata_files)
        tuple val(sample_id), val(tech_reps), val(scanmode)
+       val(preprocessing_scripts_dir)
 
     output:
-       path 'AvgPeaks_*.RData'
+       path 'AvgPeaks_*.RData', emit: average_peaks
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/AveragePeaks.R $sample_id $tech_reps $scanmode $params.preprocessing_scripts_dir
+        Rscript ${projectDir}/CustomModules/DIMS/AveragePeaks.R \
+                $sample_id \
+                $tech_reps \
+                $scanmode \
+                $preprocessing_scripts_dir
         """
 }

DIMS/CollectAveraged.nf

@@ -2,7 +2,6 @@ process CollectAveraged {
     tag "DIMS CollectAveraged"
     label 'CollectAveraged'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(averaged_files)
@@ -12,6 +11,6 @@ process CollectAveraged {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/CollectAveraged.R
+        Rscript ${projectDir}/CustomModules/DIMS/CollectAveraged.R
         """
 }

DIMS/CollectFilled.R

@@ -4,7 +4,7 @@ cmd_args <- commandArgs(trailingOnly = TRUE)
 preprocessing_scripts_dir <- cmd_args[1]
 z_score <- as.numeric(cmd_args[2])
 
-source(paste0(preprocessing_scripts_dir, "collect_filled_functions.R"))
+source(paste0(preprocessing_scripts_dir, "/collect_filled_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/CollectFilled.nf

@@ -2,18 +2,23 @@ process CollectFilled {
     tag "DIMS CollectFilled"
     label 'CollectFilled'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(filled_files)
        each path(replication_pattern)
+       val(preprocessing_scripts_dir)
+       val(ppm)
+       val(zscore)
 
     output:
        path('peakgroup_list*.txt')
        path('peakgroup_list*.RData'), emit: filled_pgrlist
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/CollectFilled.R $params.preprocessing_scripts_dir $params.zscore
+        Rscript ${projectDir}/CustomModules/DIMS/CollectFilled.R \
+                $preprocessing_scripts_dir \
+                $ppm \
+                $zscore
         """
 }

DIMS/CollectSumAdducts.R

@@ -6,7 +6,7 @@ cmd_args <- commandArgs(trailingOnly = TRUE)
 
 preprocessing_scripts_dir <- cmd_args[1]
 
-source(paste0(preprocessing_scripts_dir, "collect_sum_adducts_functions.R"))
+source(paste0(preprocessing_scripts_dir, "/collect_sum_adducts_functions.R"))
 
 # Collect all AdductSums part files for each scanmode and save to RData file
 outlist_tot_pos <- combine_sum_adduct_parts("positive")

DIMS/CollectSumAdducts.nf

@@ -2,17 +2,18 @@ process CollectSumAdducts {
     tag "DIMS CollectSumAdducts"
     label 'CollectSumAdducts'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(collect_files)
+       val(preprocessing_scripts_dir)
 
     output:
        path('AdductSums_combined.RData'), emit: adductsums_combined
        tuple path('AdductSums_positive.RData'), path('AdductSums_negative.RData'), emit: adductsums_scanmodes
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/CollectSumAdducts.R $params.preprocessing_scripts_dir
+        Rscript ${projectDir}/CustomModules/DIMS/CollectSumAdducts.R \
+                $preprocessing_scripts_dir
         """
 }

DIMS/EvaluateTics.R

@@ -16,7 +16,7 @@ thresh2remove <- 1000000000
 preprocessing_scripts_dir <- cmd_args[7]
 
 # Load functions
-source(paste0(preprocessing_scripts_dir, "evaluate_tics_functions.R"))
+source(paste0(preprocessing_scripts_dir, "/evaluate_tics_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/EvaluateTics.nf

@@ -2,7 +2,6 @@ process EvaluateTics {
     tag "DIMS EvaluateTics"
     label 'EvaluateTics'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(rdata_file)
@@ -11,24 +10,27 @@ process EvaluateTics {
        val(analysis_id)
        path(highest_mz_file)
        path(trim_params_file)
+       val(preprocessing_scripts_dir)
+       val(nr_replicates)
+       val(matrix)
 
     output:
-       path('*_repl_pattern.RData'),      emit: pattern_files
-       path('replicates_per_sample.txt'), emit: sample_techreps
-       path('miss_infusions_negative.txt')
-       path('miss_infusions_positive.txt')
-       path('*_TICplots.pdf'),            emit: tic_plots_pdf
+       path('*_repl_pattern.RData'),        emit: pattern_files
+       path('replicates_per_sample.txt'),   emit: sample_techreps
+       path('miss_infusions_negative.txt'), emit: miss_inf_neg
+       path('miss_infusions_positive.txt'), emit: miss_inf_pos
+       path('*_TICplots.pdf'),              emit: tic_plots_pdf
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/EvaluateTics.R $init_file \
-                                                             $params.nr_replicates \
-                                                             $analysis_id \
-                                                             $params.matrix \
-                                                             $highest_mz_file \
-                                                             $trim_params_file \
-                                                             $params.preprocessing_scripts_dir
+        Rscript ${projectDir}/CustomModules/DIMS/EvaluateTics.R \
+                $init_file \
+                $nr_replicates \
+                $analysis_id \
+                $matrix \
+                $highest_mz_file \
+                $trim_params_file \
+                $preprocessing_scripts_dir
         """
 }
 
-

DIMS/FillMissing.R

@@ -6,7 +6,7 @@ preprocessing_scripts_dir <- cmd_args[2]
 thresh <- as.numeric(cmd_args[3])
 
 # Load in function scripts
-source(paste0(preprocessing_scripts_dir, "fill_missing_functions.R"))
+source(paste0(preprocessing_scripts_dir, "/fill_missing_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/FillMissing.nf

@@ -2,17 +2,21 @@ process FillMissing {
     tag "DIMS FillMissing ${peakgrouplist_file}"
     label 'FillMissing'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(peakgrouplist_file)
        each path(replication_pattern)
+       val(preprocessing_scripts_dir)
+       val(threshold)
 
     output:
-       path('*_filled.RData')
+       path('*_filled.RData'), emit: filled_data
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/FillMissing.R $peakgrouplist_file $params.preprocessing_scripts_dir $params.thresh
+        Rscript ${projectDir}/CustomModules/DIMS/FillMissing.R \
+                $peakgrouplist_file \
+                $preprocessing_scripts_dir \
+                $threshold
         """
 }

DIMS/GenerateBreaks.R

@@ -7,6 +7,10 @@ cmd_args <- commandArgs(trailingOnly = TRUE)
 filepath <- cmd_args[1]
 trim <- as.numeric(cmd_args[2])
 resol <- as.numeric(cmd_args[3])
+preprocessing_scripts_dir <- cmd_args[4]
+
+# load in function script
+source(paste0(preprocessing_scripts_dir, "/generate_breaks_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/GenerateBreaks.nf

@@ -2,10 +2,12 @@ process GenerateBreaks {
     tag "DIMS GenerateBreaks"
     label 'GenerateBreaks'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        tuple(val(file_id), path(mzML_file))
+       val(trim)
+       val(resolution)
+       val(preprocessing_scripts_dir)
 
     output:
        path('breaks.fwhm.RData'), emit: breaks
@@ -14,9 +16,10 @@ process GenerateBreaks {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateBreaks.R \
+        Rscript ${projectDir}/CustomModules/DIMS/GenerateBreaks.R \
                 $mzML_file \
-                $params.trim \
-                $params.resolution 
+                $trim \
+                $resolution \
+                $preprocessing_scripts_dir
         """
 }

DIMS/GenerateExcel.R

@@ -16,7 +16,7 @@ export_scripts_dir <- cmd_args[4]
 path_metabolite_groups <- cmd_args[5]
 
 # Load in function scripts
-source(paste0(export_scripts_dir, "generate_excel_functions.R"))
+source(paste0(export_scripts_dir, "/generate_excel_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/GenerateExcel.nf

@@ -2,12 +2,14 @@ process GenerateExcel {
     tag "DIMS GenerateExcel"
     label 'GenerateExcel'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(adductsums_combined)
-       val(analysis_id) 
        path(relevance_file)
+       val(analysis_id) 
+       val(export_scripts_dir)
+       val(path_metabolite_groups)
+       val(zscore)
 
     output:
        path("outlist.RData"), emit: outlist_zscores
@@ -20,6 +22,11 @@ process GenerateExcel {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateExcel.R $analysis_id $relevance_file $params.zscore $params.export_scripts_dir $params.path_metabolite_groups
+        Rscript ${projectDir}/CustomModules/DIMS/GenerateExcel.R \
+                $analysis_id \
+                $relevance_file \
+                $zscore \
+                $export_scripts_dir \
+                $path_metabolite_groups
         """
 }

DIMS/GenerateQCOutput.R

@@ -14,7 +14,7 @@ sst_components_file <- cmd_args[4]
 export_scripts_dir <- cmd_args[5]
 
 # Load in function scripts
-source(paste0(export_scripts_dir, "generate_qc_output_functions.R"))
+source(paste0(export_scripts_dir, "/generate_qc_output_functions.R"))
 
 # Initialize
 options(digits = 16)

DIMS/GenerateQCOutput.nf

@@ -2,14 +2,17 @@ process GenerateQCOutput {
     tag "DIMS GenerateQCOutput"
     label 'GenerateQCOutput'
     container = 'ghcr.io/umcugenetics/dims:v1.4.0'
-    shell = ['/bin/bash', '-euo', 'pipefail']
 
     input:
        path(outlist_zscores)
        path(adductsums_scanmodes)
        path(identified_files)
        path(init_file) 
        val(analysis_id)
+       val(sst_components_file)
+       val(export_scripts_dir)
+       val(zscore)
+       val(matrix)
 
     output:
        tuple path('*_IS_results.RData'), path('*_positive_control.RData'), optional: true
@@ -22,10 +25,11 @@ process GenerateQCOutput {
 
     script:
         """
-        Rscript ${baseDir}/CustomModules/DIMS/GenerateQCOutput.R $init_file \
-                                                                 $analysis_id \
-                                                                 $params.matrix \
-                                                                 $params.sst_components_file \
-                                                                 $params.export_scripts_dir
+        Rscript ${projectDir}/CustomModules/DIMS/GenerateQCOutput.R \
+                $init_file \
+                $analysis_id \
+                $matrix \
+                $sst_components_file \
+                $export_scripts_dir
         """
 }

DIMS/GenerateViolinPlots.R

@@ -37,7 +37,7 @@ number_of_metabolites <- list(
 )
 
 # Load functions
-source(paste0(export_scripts_dir, "generate_violin_plots_functions.R"))
+source(paste0(export_scripts_dir, "/generate_violin_plots_functions.R"))
 
 # Load dataframe with intensities and Z-scores for all samples
 intensities_zscore_df <- get(load("outlist.RData"))