Initialize foldseek pipeline for WES

nextflow.config

@@ -0,0 +1,43 @@
+// Manifest for Nextflow metadata
+manifest {
+    name = 'Foldseek-Nextflow'
+    author = 'Generated from Foldseek repository'
+    homePage = 'https://github.com/steineggerlab/foldseek'
+    description = 'Nextflow pipeline for Foldseek - Fast protein structure search and clustering'
+    mainScript = 'main.nf'
+    version = '1.0.0'
+}
+
+// Global default parameters
+params {
+    query = "/mnt/OmicNAS/private/old/olamide/foldseek/input/1CRN.pdb"
+    target = "/mnt/OmicNAS/private/old/olamide/foldseek/input/"
+    outdir = "/mnt/OmicNAS/private/old/olamide/foldseek/output"
+    mode = "search"
+    sensitivity = 9.5
+    evalue = 0.001
+    threads = 4
+    alignment_type = 2
+    coverage = 0.0
+    format_output = "query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits"
+}
+
+// Container configurations
+docker {
+    enabled = true
+    runOptions = '-v /mnt:/mnt'
+}
+
+// Process configurations
+process {
+    cpus = 4
+    memory = '16 GB'
+}
+
+// Execution configurations
+executor {
+    $local {
+        cpus = 8
+        memory = '32 GB'
+    }
+}