From f45a32bb2a362a038f75eb5d8ecfd76c2c9f504f Mon Sep 17 00:00:00 2001 From: Charlotte Soneson Date: Sun, 28 Apr 2024 15:27:44 +0200 Subject: [PATCH] Move path normalization --- R/runDIANNAnalysis.R | 12 ++++++------ R/runFragPipeAnalysis.R | 10 +++++----- R/runMaxQuantAnalysis.R | 12 ++++++------ R/runPDTMTAnalysis.R | 12 ++++++------ R/runPDTMTptmAnalysis.R | 12 ++++++------ R/runSpectronautAnalysis.R | 12 ++++++------ 6 files changed, 35 insertions(+), 35 deletions(-) diff --git a/R/runDIANNAnalysis.R b/R/runDIANNAnalysis.R index e4812a1..db6a074 100644 --- 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 index 7562f52..0daeb3c 100755 --- 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 index df0392e..6df77d3 100644 --- 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 index 6926e82..7f6cf5b 100644 --- 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 index 4ac309d..b18b287 100644 --- 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 index 54c47ad..9c961df 100644 --- 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 ## -------------------------------------------------------------------------