Move path normalization

fmicompbio · Apr 28, 2024 · f45a32b · f45a32b
1 parent 2c4c7dd
commit f45a32b
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Showing 6 changed files with 35 additions and 35 deletions.
diff --git a/R/runDIANNAnalysis.R b/R/runDIANNAnalysis.R
@@ -149,12 +149,6 @@ runDIANNAnalysis <- function(
     complexSpecies = "all", complexDbPath = NULL, stringVersion = "11.5",
     stringDir = NULL, linkTableColumns = c(), customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize paths
-    ## -------------------------------------------------------------------------
-    diannFile <- normalizePath(diannFile)
-    diannLogFile <- normalizePath(diannLogFile)
-
     ## -------------------------------------------------------------------------
     ## Fix ctrlGroup/mergeGroups
     ## -------------------------------------------------------------------------
@@ -218,6 +212,12 @@ runDIANNAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize paths
+    ## -------------------------------------------------------------------------
+    diannFile <- normalizePath(diannFile)
+    diannLogFile <- normalizePath(diannLogFile)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------

diff --git a/R/runFragPipeAnalysis.R b/R/runFragPipeAnalysis.R
@@ -99,11 +99,6 @@ runFragPipeAnalysis <- function(
     complexSpecies = "all", complexDbPath = NULL, stringVersion = "11.5",
     stringDir = NULL, linkTableColumns = c(), customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize path
-    ## -------------------------------------------------------------------------
-    fragpipeDir <- normalizePath(fragpipeDir)
-
     ## -------------------------------------------------------------------------
     ## Fix ctrlGroup/mergeGroups
     ## -------------------------------------------------------------------------
@@ -166,6 +161,11 @@ runFragPipeAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize path
+    ## -------------------------------------------------------------------------
+    fragpipeDir <- normalizePath(fragpipeDir)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------

diff --git a/R/runMaxQuantAnalysis.R b/R/runMaxQuantAnalysis.R
@@ -278,12 +278,6 @@ runMaxQuantAnalysis <- function(
     complexSpecies = "all", complexDbPath = NULL, stringVersion = "11.5",
     stringDir = NULL, linkTableColumns = c(), customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize paths
-    ## -------------------------------------------------------------------------
-    mqFile <- normalizePath(mqFile)
-    mqParameterFile <- normalizePath(mqParameterFile)
-
     ## -------------------------------------------------------------------------
     ## Fix ctrlGroup/mergeGroups
     ## -------------------------------------------------------------------------
@@ -347,6 +341,12 @@ runMaxQuantAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize paths
+    ## -------------------------------------------------------------------------
+    mqFile <- normalizePath(mqFile)
+    mqParameterFile <- normalizePath(mqParameterFile)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------

diff --git a/R/runPDTMTAnalysis.R b/R/runPDTMTAnalysis.R
@@ -148,12 +148,6 @@ runPDTMTAnalysis <- function(
     stringDir = NULL, linkTableColumns = c(),
     customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize paths
-    ## -------------------------------------------------------------------------
-    pdOutputFolder <- normalizePath(pdOutputFolder)
-    pdAnalysisFile <- normalizePath(pdAnalysisFile)
-
     ## -------------------------------------------------------------------------
     ## Fix ctrlGroup/mergeGroups
     ## -------------------------------------------------------------------------
@@ -224,6 +218,12 @@ runPDTMTAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize paths
+    ## -------------------------------------------------------------------------
+    pdOutputFolder <- normalizePath(pdOutputFolder)
+    pdAnalysisFile <- normalizePath(pdAnalysisFile)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------

diff --git a/R/runPDTMTptmAnalysis.R b/R/runPDTMTptmAnalysis.R
@@ -146,12 +146,6 @@ runPDTMTptmAnalysis <- function(
         interactiveGroupColumn = NULL,
         seed = 42, linkTableColumns = c(), customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize paths
-    ## -------------------------------------------------------------------------
-    sceProteins <- normalizePath(sceProteins)
-    scePeptides <- normalizePath(scePeptides)
-
     ## -------------------------------------------------------------------------
     ## Check arguments
     ## -------------------------------------------------------------------------
@@ -184,6 +178,12 @@ runPDTMTptmAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize paths
+    ## -------------------------------------------------------------------------
+    sceProteins <- normalizePath(sceProteins)
+    scePeptides <- normalizePath(scePeptides)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------

diff --git a/R/runSpectronautAnalysis.R b/R/runSpectronautAnalysis.R
@@ -91,12 +91,6 @@ runSpectronautAnalysis <- function(
     complexSpecies = "all", complexDbPath = NULL, stringVersion = "11.5",
     stringDir = NULL, linkTableColumns = c(), customYml = NULL, doRender = TRUE
 ) {
-    ## -------------------------------------------------------------------------
-    ## Normalize paths
-    ## -------------------------------------------------------------------------
-    spectronautFile <- normalizePath(spectronautFile)
-    spectronautLogFile <- normalizePath(spectronautLogFile)
-
     ## -------------------------------------------------------------------------
     ## Fix ctrlGroup/mergeGroups
     ## -------------------------------------------------------------------------
@@ -160,6 +154,12 @@ runSpectronautAnalysis <- function(
     ## Gives a warning if pandoc and/or pandoc-citeproc is not available
     pandocOK <- .checkPandoc(ignorePandoc = TRUE)
 
+    ## -------------------------------------------------------------------------
+    ## Normalize paths
+    ## -------------------------------------------------------------------------
+    spectronautFile <- normalizePath(spectronautFile)
+    spectronautLogFile <- normalizePath(spectronautLogFile)
+
     ## -------------------------------------------------------------------------
     ## Copy Rmd template and insert arguments
     ## -------------------------------------------------------------------------