add nextflow d30e48d

nextflow/tests/blast.nf

@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+params.db = "$baseDir/blast-db/tiny"
+params.query = "$baseDir/data/sample.fa"
+params.chunkSize = 1
+
+process blast {
+    input:
+    path 'seq.fa'
+    val db
+
+    output:
+    path 'out'
+
+    script:
+    """
+    blastp -db $db -query seq.fa -outfmt 6 > out
+    """
+}
+
+process sort {
+    input:
+    path 'hits_*'
+
+    output:
+    stdout
+
+    script:
+    """
+    sort hits_*
+    """
+}
+
+
+workflow {
+    ch_fasta = channel.fromPath(params.query)
+        | splitFasta( by: params.chunkSize, file:true )
+
+    blast(ch_fasta, params.db)
+        | collect
+        | sort
+        | subscribe { hits -> println hits }
+}