FIX: add missing parameter for gffred in config

GenomiqueENS · Nov 14, 2024 · 0c1d7a6 · 0c1d7a6
1 parent 3947783
commit 0c1d7a6
Showing 1 changed file with 9 additions and 6 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -8,22 +8,25 @@
 
 params {
  	// Input options
-    reads               = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/menelaus/*.fastq.gz"
-    samplesheet         = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/menelaus/samplesheet.csv"
+    reads               = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/achilles/*.fastq"
+    samplesheet         = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/achilles/samplesheet.csv"
 
  	// References
     //genome = "${launchDir}/data/hdujardini_HiC"
     //annotation = "${launchDir}/data/hdujardini_HiC"
-    genome              = "/import/rhodos10/ressources/sequencages/genomes/morphomen1.fa.bz2"
-    annotation          = "/import/rhodos10/ressources/sequencages/annotations/morphomen1.gff.bz2"
+    genome              = "/import/rhodos10/ressources/sequencages/genomes/morphoach1.fa.bz2"
+    annotation          = "/import/rhodos10/ressources/sequencages/annotations/morphoach1.gff.bz2"
 
     // Orientation of FASTQ files
     oriented            = true  // if reads already oriented, replace with oriented = true
-    sam                 = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/menelaus/*.sam"  // if oriented = true, provide sam files from eoulsan
+    sam                 = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/achilles/*.sam"  // if oriented = true, provide sam files from eoulsan
 
     // Restrander configuration file (TSO and RTP sequences)
     config              = "${launchDir}/assets/PCB111.json"
 
+    // GFFRead input parameters
+    gffread_parameters = "-M"
+
     // Minimap2 intron length
     intron_length       = "20000" // 200k by default
     junc_bed            = null 	// if no junk bed, replace with optional_shortread = null
@@ -35,7 +38,7 @@ params {
     optional_shortread  = null  	// if no short reads, replace with optional_shortread = null
 
  	// Output directory
-    outdir              = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/menelaus/result"
+    outdir              = "/import/pontos01/analyses/OUTOFTHEBLUE_C2024/egzotek/achilles/result"
 }
 
 docker {