Add Nextflow language support (#3870)

* Added nextflow language
* Added main.nf to list of filenames
* Fixed duplicate groovy scope
* Removed hello-world example
* Update grammar submodule
* Removed main.nf from filenames
* Added nextflow.config example

samples/Nextflow/blast.nf

@@ -0,0 +1,67 @@
+#!/usr/bin/env nextflow
+/*
+ * This is free and unencumbered software released into the public domain.
+ * 
+ * Anyone is free to copy, modify, publish, use, compile, sell, or
+ * distribute this software, either in source code form or as a compiled
+ * binary, for any purpose, commercial or non-commercial, and by any
+ * means.
+ * 
+ * In jurisdictions that recognize copyright laws, the author or authors
+ * of this software dedicate any and all copyright interest in the
+ * software to the public domain. We make this dedication for the benefit
+ * of the public at large and to the detriment of our heirs and
+ * successors. We intend this dedication to be an overt act of
+ * relinquishment in perpetuity of all present and future rights to this
+ * software under copyright law.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ * 
+ * For more information, please refer to <http://unlicense.org/>
+ */
+ 
+/* 
+ * Author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
+ */
+
+
+params.query = "$HOME/sample.fa"
+params.db = "$HOME/tools/blast-db/pdb/pdb"
+
+process blast {
+    output:
+     file top_hits
+
+    """
+    blastp -query ${params.query} -db ${params.db} -outfmt 6 \
+    | head -n 10 \
+    | cut -f 2 > top_hits
+    """
+}
+
+process extract {
+    input:
+     file top_hits
+    output:
+     file sequences
+
+    """
+    blastdbcmd -db ${params.db} -entry_batch $top_hits > sequences
+    """
+}
+
+process align {
+    input:
+     file sequences
+    echo true
+
+    """
+    t_coffee $sequences 2>&- | tee align_result
+    """
+}