From 40b536e51552b9250c51c42d86be2a29a19e5f8a Mon Sep 17 00:00:00 2001
From: Toni Hermoso Pulido <toniher@cau.cat>
Date: Mon, 21 Oct 2024 18:27:36 +0200
Subject: [PATCH] moved basedDir to projectDir

---
 README.md                            | 14 +++++++-------
 main.nf                              |  2 +-
 modules/local/exorthist/plot/plot.nf |  2 +-
 nextflow.config                      |  4 ++--
 4 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/README.md b/README.md
index 587a757..15c65db 100644
--- a/README.md
+++ b/README.md
@@ -142,20 +142,20 @@ For the pipeline to run, a `params.config` file with the following format has to
 
 ```
 params {
-    cluster        = "$baseDir/test/hg38_mm10_bosTau9.tab"
-    genomes        = "$baseDir/test/GENOMES/*_gDNA.fasta.gz"
-    annotations    = "$baseDir/test/GTF/*_annot.gtf.gz"
+    cluster        = "$projectDir/test/hg38_mm10_bosTau9.tab"
+    genomes        = "$projectDir/test/GENOMES/*_gDNA.fasta.gz"
+    annotations    = "$projectDir/test/GTF/*_annot.gtf.gz"
     alignmentnum   = 1000
     orthogroupnum  = 500
     extraexons     = ""
     bonafide_pairs = ""
     orthopairs     = ""
-    evodists       = "$baseDir/test/evodists.txt"
+    evodists       = "$projectDir/test/evodists.txt"
     long_dist      = "2,0.10,0.40,0.15"
     medium_dist    = "2,0.30,0.60,0.20"
     short_dist     = "2,0.50,0.60,0.25"
     prevaln        = ""
-    output         = "$baseDir/output_test"
+    output         = "$projectDir/output_test"
     email          = "yourmail@yourdomain"
 }
 ```
@@ -496,8 +496,8 @@ A template of the params.config file is provided together with the pipeline.
 ```
 params {
     geneID          = "ENSG00000159055"
-    output          = "$baseDir/../output_test"
-    output_plot     = "$baseDir/output_exint"
+    output          = "$projectDir/../output_test"
+    output_plot     = "$projectDir/output_exint"
     relevant_exs    = "chr21:32274830-32274896"
     ordered_species = "hg38,mm10,bosTau9"
     isoformID       = "ENSP00000290130"
diff --git a/main.nf b/main.nf
index 938b45b..477f054 100644
--- a/main.nf
+++ b/main.nf
@@ -149,7 +149,7 @@ workflow {
         gtfs = Channel.fromPath(params.annotations).collect()
         fastas = Channel.fromPath(params.genomes).collect()
 
-        blosumfile = Channel.fromPath("${baseDir}/files/blosum62.txt", checkIfExists: true).collect()
+        blosumfile = Channel.fromPath("${projectDir}/files/blosum62.txt", checkIfExists: true).collect()
 
         // TODO: Review this in an easier way
         gtfs_suffix = Channel.fromFilePairs(params.annotations, size: 1).flatten().collate(2).map{[it[1].getName().toString().split(it[0].toString())[1]]}.unique().flatten()
diff --git a/modules/local/exorthist/plot/plot.nf b/modules/local/exorthist/plot/plot.nf
index 4eb9626..013a3b9 100644
--- a/modules/local/exorthist/plot/plot.nf
+++ b/modules/local/exorthist/plot/plot.nf
@@ -19,6 +19,6 @@ process PLOT_EXINT {
 
     script:
     """
-    Rscript $baseDir/bin/exint_plotter.R ${my_geneID} ${my_query_species} ${baseDir}/bin ${gene_clusters} ${ordered_target} ${isoform_interesting_exs} ${relevant_exons}
+    Rscript ${projectDir}/bin/exint_plotter.R ${my_geneID} ${my_query_species} ${projectDir}/bin ${gene_clusters} ${ordered_target} ${isoform_interesting_exs} ${relevant_exons}
     """
 }
diff --git a/nextflow.config b/nextflow.config
index d800688..089a225 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,7 @@ plugins {
   id 'nf-schema@2.0.0'
 }
 
-includeConfig "$baseDir/params.config"
+includeConfig "$projectDir/params.config"
 
 
 process {
@@ -63,7 +63,7 @@ process {
 
 process.container = 'perl:5.24-threaded-buster'
 //singularity.enabled = true
-singularity.cacheDir = "$baseDir/singularity"
+singularity.cacheDir = "$projectDir/singularity"
 
 // Modify accordig to cloud parameters
 profiles {