Merge pull request #23 from Juke34/reditools3

Reditools3: logging and threads

Author: eascarrunz

config/ressources/hpc.config

@@ -28,4 +28,8 @@ process {
         cpus = 8
         time = '4d'
     }
+    withName: 'reditools3' {
+        cpus = 6
+        time = '4d'
+    }
 }

config/ressources/local.config

@@ -18,6 +18,11 @@ process {
         memory = "4G"
         time = '1d'
     }
+    withLabel: 'agat' {
+        cpus = 1
+        memory = "2G"
+        time = '1d'
+    }
     withLabel: 'hisat2_index' {
         cpus = 4
         time = '1h'
@@ -35,7 +40,13 @@ process {
         time = '1d'
     }
     withLabel: 'bamutil' {
+        cpus = 1
+        time = '1d'
+        memory="12G"
+    }    
+    withLabel: 'reditools3' {
         cpus = 2
         time = '1d'
+        memory="4G"
     }    
 }

modules/reditools3.nf

@@ -8,7 +8,8 @@ process reditools3 {
         path genome
 
     output:
-        tuple(val(meta), path("edit_table.txt"), emit: tuple_sample_serial_table)
+        tuple(val(meta), path("${base_name}.site_edits_reditools3.txt"), emit: tuple_sample_serial_table)
+        path("${base_name}.reditools3.log", emit: log)
 
     script:
         // Set the strand orientation parameter from the library type parameter
@@ -27,8 +28,9 @@ process reditools3 {
             // the reditools error message
             strand_orientation = meta.libtype
         }
+        base_name = bam.BaseName
 
         """
-        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file edit_table.txt
+        python -m reditools analyze ${bam} --reference ${genome} --strand ${strand_orientation} --output-file ${base_name}.site_edits_reditools3.txt --threads ${task.cpus} --verbose > ${base_name}.reditools3.log
         """
 }