Fix strict syntax errors, add CI test

.github/workflows/build.yml

@@ -0,0 +1,41 @@
+name: blast ci
+on: [push]
+
+jobs:
+  build:
+    name: blast ci
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        java_version: ['17']
+        nextflow_version: ['23.10']
+
+    steps:
+      - name: Environment
+        run: env | sort
+
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: Setup Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: ${{ matrix.java_version }}
+          architecture: x64
+
+      - name: Setup Nextflow ${{ matrix.nextflow_version }}
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
+        with:
+          version: "${{ matrix.nextflow_version }}"
+
+      - name: Tests
+        run: |
+          nextflow run . -profile docker
+        env:
+          NXF_ANSI_LOG: false

.gitignore

@@ -1,4 +1,3 @@
 .git
-work
 .nextflow*
-git push -u origin master
+work

README.md

@@ -1,20 +1,24 @@
-# Blast example 
+# Blast example
 
-A basic Blast pipeline using Nextflow 
+A basic Blast pipeline using Nextflow.
 
-[![Build Status](https://travis-ci.org/nextflow-io/blast-example.svg?branch=master)](https://travis-ci.org/nextflow-io/blast-example)
+[![nextflow](https://img.shields.io/badge/nextflow-%E2%89%A523.10-brightgreen.svg)](http://nextflow.io)
 
-## Get started 
+## Get started
 
-Install Nextflow 
+Install Nextflow
 
-    curl https://get.nextflow.io | bash 
+```bash
+curl https://get.nextflow.io | bash
+```
 
-Run the script 
+Run the pipeline:
 
-    nextflow run blast-example -with-docker
+```bash
+nextflow run blast-example -profile docker
+```
 
-## Dependencies 
+## Dependencies
 
-* Java 11 or later 
-* Docker 1.10 or later 
+* Java 17 or later
+* Docker

main.nf

@@ -20,43 +20,41 @@
  *   You should have received a copy of the GNU General Public License
  *   along with Nextflow.  If not, see <http://www.gnu.org/licenses/>.
  */
- 
+
 
 /*
- * Defines the pipeline inputs parameters (giving a default value for each for them) 
- * Each of the following parameters can be specified as command line options
+ * Defines the pipeline parameters (with a default value for each one)
+ * Each parameter can be specified on the command line (e.g. `--query query.fa`)
  */
-params.query = "$baseDir/data/sample.fa"
-params.db = "$baseDir/blast-db/pdb/tiny"
+params.query = "$projectDir/data/sample.fa"
+params.db = "$projectDir/blast-db/pdb/tiny"
 params.out = "result.txt"
-params.chunkSize = 100 
-
-db_name = file(params.db).name
-db_dir = file(params.db).parent
+params.chunkSize = 100
 
 
 workflow {
+    db_dir = file(params.db).parent
+    db_name = file(params.db).name
+
     /*
      * Create a channel emitting the given query fasta file(s).
      * Split the file into chunks containing as many sequences as defined by the parameter 'chunkSize'.
      * Finally, assign the resulting channel to the variable 'ch_fasta'
      */
-    Channel
-        .fromPath(params.query)
-        .splitFasta(by: params.chunkSize, file:true)
-        .set { ch_fasta }
+    ch_fasta = channel.fromPath(params.query)
+        .splitFasta(by: params.chunkSize, file: true)
 
     /*
      * Execute a BLAST job for each chunk emitted by the 'ch_fasta' channel
      * and emit the resulting BLAST matches.
      */
-    ch_hits = blast(ch_fasta, db_dir)
+    ch_hits = blast(ch_fasta, db_dir, db_name)
 
     /*
      * Each time a file emitted by the 'blast' process, an extract job is executed,
      * producing a file containing the matching sequences.
      */
-    ch_sequences = extract(ch_hits, db_dir)
+    ch_sequences = extract(ch_hits, db_dir, db_name)
 
     /*
      * Collect all the sequences files into a single file
@@ -71,13 +69,15 @@ workflow {
 process blast {
     input:
     path 'query.fa'
-    path db
+    path db_dir
+    val db_name
 
     output:
     path 'top_hits'
 
+    script:
     """
-    blastp -db $db/$db_name -query query.fa -outfmt 6 > blast_result
+    blastp -db $db_dir/$db_name -query query.fa -outfmt 6 > blast_result
     cat blast_result | head -n 10 | cut -f 2 > top_hits
     """
 }
@@ -86,12 +86,14 @@ process blast {
 process extract {
     input:
     path 'top_hits'
-    path db
+    path db_dir
+    val db_name
 
     output:
     path 'sequences'
 
+    script:
     """
-    blastdbcmd -db $db/$db_name -entry_batch top_hits | head -n 10 > sequences
+    blastdbcmd -db $db_dir/$db_name -entry_batch top_hits | head -n 10 > sequences
     """
 }

nextflow.config

@@ -1,7 +1,13 @@
 manifest {
-  nextflowVersion = '>= 22.04.0'
+  nextflowVersion = '>= 23.10.0'
 }
 
 process {
   container = 'nextflow/examples'
-}
+}
+
+profiles {
+  docker {
+    docker.enabled = true
+  }
+}