Fixed hite

Author: FernandoDuarteF

conf/modules.config

@@ -308,31 +308,17 @@ process {
 
     withName: 'HITE' {
         ext.args = '--annotate 1'
+        containerOptions = {
+          (workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) ? 
+          "--bind \$TMPDIR:\$TMPDIR" : 
+          "--volume \$TMPDIR:\$TMPDIR}"
+        }
         publishDir = [
-            path: { "${params.outdir}/hite" },
-            mode: params.publish_dir_mode,
-            enable: false
+            path: { "${params.outdir}/hite/${meta.id}" },
+            mode: params.publish_dir_mode
         ]
     }
 
-//    withName: 'REPEATMASKER_REPEATMASKER' {
-//        ext.args = { params.species ? "-species ${params.species}" : ''}
-//        containerOptions = { 
-//            if (params.famdb_library) {
-//                workflow.containerEngine == 'docker' ? // If docker is used, mount the famdb library using --volume
-//                "--volume ${params.famdb_library}:/opt/RepeatMasker/Libraries/famdb --env LIBDIR=/opt/RepeatMasker/Libraries" : 
-//                (workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ) ? // If singularity or apptainer is used, mount the famdb library using --bind
-//                "--bind ${params.famdb_library}:/opt/RepeatMasker/Libraries/famdb --env LIBDIR=/opt/RepeatMasker/Libraries" : ''
-//            } else {
-//              ''
-//            }
-//        }
-//        publishDir = [
-//            path: { "${params.outdir}/repeatmasker" },
-//            mode: params.publish_dir_mode,
-//        ]
-//    }
-
 
     withName: 'CDHIT_CDHITEST' {
         ext.args = '-d 0 -aS 0.8 -c 0.8 -G 0 -g 1 -b 500 -r 1'
@@ -343,4 +329,37 @@ process {
         ]
     }
 
+    withName: 'FAMDB_PY' {
+        publishDir = [
+            path: { "${params.outdir}/famdb.py" },
+            mode: params.publish_dir_mode,
+            enable: false
+        ]
+    }
+
+    withName: 'REPEATMODELER_BUILDDATABASE' {
+        publishDir = [
+            path: { "${params.outdir}/repeatmodeler/buildb" },
+            mode: params.publish_dir_mode,
+            enable: false
+        ]
+    }
+
+    withName: 'REPEATMODELER_REPEATMODELER' {
+        publishDir = [
+            path: { "${params.outdir}/repeatmodeler/repeatmodeler/${meta.id}" },
+            mode: params.publish_dir_mode,
+            enable: false
+        ]
+    }
+
+    withName: 'REPEATMASKER_REPEATMASKER' {
+        publishDir = [
+            path: { "${params.outdir}/repeatmasker/${meta.id}" },
+            mode: params.publish_dir_mode,
+            //enable: false
+        ]
+    }
+
+
 }

modules/local/hite/main.nf

@@ -41,7 +41,7 @@ process HITE {
     --genome \${newpath} \\
     --out_dir \${mydir}/${prefix}_hite_results \\
     --thread ${task.cpus} \\
-    --work_dir \$TMPDIR
+    --work_dir \$TMPDIR \\
     $args
 
     cat <<-END_VERSIONS > \${mydir}/versions.yml