fix: switch workDir to projectDir in nextflow.config

CCBR · Jan 25, 2024 · af4720c · af4720c
1 parent 5ae6934
commit af4720c
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -40,14 +40,14 @@ params {
     }
 
     multiqc {
-        config = "${workDir}/assets/multiqc_config.yaml"
-        logo = "${workDir}/assets/ccbr_logo.png"
+        config = "${projectDir}/assets/multiqc_config.yaml"
+        logo = "${projectDir}/assets/ccbr_logo.png"
     }
 
     min_fragment_length = 200 // https://github.com/CCBR/Pipeliner/blob/86c6ccaa3d58381a0ffd696bbf9c047e4f991f9e/Rules/InitialChIPseqQC.snakefile#L539
 
     gem {
-        read_dists = "${workDir}/assets/gem/Read_Distribution_default.txt" // source https://groups.csail.mit.edu/cgs/gem/download/Read_Distribution_default.txt
+        read_dists = "${projectDir}/assets/gem/Read_Distribution_default.txt" // source https://groups.csail.mit.edu/cgs/gem/download/Read_Distribution_default.txt
         fold = 3
         k_min = 6
         k_max = 13
@@ -67,11 +67,11 @@ params {
     }
     homer {
         de_novo = true
-        jaspar_db = "${workDir}/assets/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt" // source https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt
+        jaspar_db = "${projectDir}/assets/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt" // source https://jaspar.genereg.net/download/data/2022/CORE/JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt
     }
 
     diffbind {
-        report = "${workDir}/assets/diffbind_report.Rmd"
+        report = "${projectDir}/assets/diffbind_report.Rmd"
     }
 
     run { // some steps can be turned on/off for debugging purposes