Make tests comply with strict syntax

docs/snippets/process-out-eval.nf

@@ -2,6 +2,7 @@ process sayHello {
     output:
     eval('bash --version')
 
+    script:
     """
     echo Hello world!
     """

docs/snippets/process-stdout.nf

@@ -2,6 +2,7 @@ process sayHello {
     output:
     stdout
 
+    script:
     """
     echo Hello world!
     """

docs/snippets/your-first-script.nf

@@ -4,6 +4,7 @@ process splitLetters {
     output:
     path 'chunk_*'
 
+    script:
     """
     printf '${params.str}' | split -b 6 - chunk_
     """
@@ -16,6 +17,7 @@ process convertToUpper {
     output:
     stdout
 
+    script:
     """
     cat $x | tr '[a-z]' '[A-Z]'
     """

tests/ampa-dsl2.nf

@@ -15,17 +15,17 @@ process ampaTask {
     output:
     path 'result'
 
-    // The BASH script to be executed - for each - sequence
+    script:
     """
     AMPA.pl -in=${seq} -noplot -rf=result -df=data
     """
 
 }
 
 workflow {
-    Channel.fromPath(params.in) |
-            splitFasta(file:true) |
-            ampaTask |
-            view { it.text }
+    Channel.fromPath(params.in)
+        | splitFasta(file:true)
+        | ampaTask
+        | view { file -> file.text }
 }
 

tests/basic-dsl2.nf

@@ -17,6 +17,7 @@ process splitSequences {
     output:
     path 'seq_*'
 
+    script:
     """
     awk '/^>/{f="seq_"++d} {print > f}' < input.fa
     """
@@ -34,6 +35,7 @@ process reverse {
     output:
     stdout
 
+    script:
     """
     cat $x | rev
     """

tests/blast-dsl2.nf

@@ -4,17 +4,17 @@ params.db = "$baseDir/blast-db/tiny"
 params.query = "$baseDir/data/sample.fa"
 params.chunkSize = 1
 
-DB = file(params.db)
-
 process blast {
     input:
     path 'seq.fa'
+    path db
 
     output:
     path 'out'
 
+    script:
     """
-    blastp -db $DB -query seq.fa -outfmt 6 > out
+    blastp -db $db -query seq.fa -outfmt 6 > out
     """
 }
 
@@ -25,17 +25,19 @@ process sort {
     output:
     stdout
 
+    script:
     """
     sort hits_*
     """
 }
 
 
 workflow {
-    Channel.fromPath(params.query) |
-            splitFasta( by: params.chunkSize, file:true ) |
-            blast |
-            collect |
-            sort |
-            subscribe { println it }
+    ch_fasta = Channel.fromPath(params.query)
+        | splitFasta( by: params.chunkSize, file:true )
+
+    blast(ch_fasta, file(params.db))
+        | collect
+        | sort
+        | subscribe { hits -> println hits }
 }

tests/blast-parallel-dsl2.nf

@@ -4,18 +4,18 @@ params.db = "$baseDir/blast-db/tiny"
 params.query = "$baseDir/data/sample.fa"
 params.chunk = 1 
 
-db = file(params.db)
-
 /* 
  * Extends a BLAST query for each entry in the 'chunks' channel 
  */
 process blast {
     input:
     path 'query.fa'
+    path db
 
     output:
-    path top_hits
+    path 'top_hits'
 
+    script:
     """
     blastp -db ${db} -query query.fa -outfmt 6 > blast_result
     cat blast_result | head -n 10 | cut -f 2 > top_hits
@@ -28,11 +28,15 @@ process blast {
 process extract {
     input:
     path top_hits
+    path db
 
     output:
     path 'sequences'
 
-    "blastdbcmd -db ${db} -entry_batch top_hits | head -n 10 > sequences"
+    script:
+    """
+    blastdbcmd -db ${db} -entry_batch top_hits | head -n 10 > sequences
+    """
 }
 
 
@@ -45,18 +49,24 @@ process align {
     input:
     path all_seq
 
-    "t_coffee $all_seq 2>/dev/null | tee align_result"
+    script:
+    """
+    t_coffee $all_seq 2>/dev/null | tee align_result
+    """
 }
 
 /*
  * main flow
  */
 workflow {
-    Channel.fromPath(params.query) |
-            splitFasta(by: params.chunk, file:true) |
-            blast |
-            extract |
-            collectFile(name:'all_seq') |  // Collect all hits to a single file called  'all_seq'
-            align
+    db = file(params.db)
+
+    ch_fasta = Channel.fromPath(params.query)
+        | splitFasta(by: params.chunk, file:true)
+
+    ch_sequences = blast(ch_fasta, db)
 
+    extract(ch_sequences, db)
+        | collectFile(name:'all_seq') // Collect all hits to a single file called  'all_seq'
+        | align
 }

tests/buffer-dsl2.nf

@@ -6,6 +6,7 @@ process blastThemAll {
     input:
     path x
 
+    script:
     """
     echo $x
     """

tests/cache-bak.nf

@@ -4,5 +4,7 @@ workflow {
 
 process foo {
   debug true
+
+  script:
   /echo Hello world/
 }

tests/chunk-dsl2.nf

@@ -8,11 +8,12 @@ process foo {
     input:
     stdin()
 
+    script:
     "cat -"
 }
 
 workflow {
-    Channel.from(stdin) \
+    Channel.of(stdin) \
             | splitFasta( by: params.chunkSize) \
             | foo
 }

tests/collect-file.nf

@@ -15,12 +15,11 @@
  * limitations under the License.
  */
 
-Channel
-    .from('alpha', 'beta', 'gamma')
+Channel.of('alpha', 'beta', 'gamma')
     .collectFile(name: 'sample.txt', newLine: true)
-    .subscribe {
-        println "Entries are saved to file: $it"
-        println "File content is: ${it.text}"
+    .subscribe { file ->
+        println "Entries are saved to file: file"
+        println "File content is: ${file.text}"
     }
 
 println 123

tests/collect_and_merge.nf

@@ -19,7 +19,7 @@
 /*
  * fake alignment step producing a BAM and BAI files
  */
-process algn {
+process align {
   debug true
 
   input:
@@ -29,10 +29,10 @@ process algn {
   output:
   tuple val(barcode), val(seq_id), file('bam'), file('bai')
 
+  script:
   """
   echo BAM $seq_id - $barcode > bam
   echo BAI $seq_id - $barcode > bai
-
   """
 }
 
@@ -44,44 +44,48 @@ process merge {
   debug true
 
   input:
-  tuple val(barcode), val(seq_id), file(bam: 'bam?'), file(bai: 'bai?')
+  tuple val(barcode), val(seq_id), path(bam), path(bai)
 
+  script:
   """
   echo barcode: $barcode
   echo seq_ids: $seq_id
   echo bam    : $bam
   echo bai    : $bai
   """
-
 }
 
 workflow {
   def ch1 = channel.of('alpha', 'gamma')
   def ch2 = channel.of('one', 'two', 'three')
 
-  aggregation = algn(ch1, ch2)
+  aggregation = align(ch1, ch2)
 
   /*
    * aggregation is made by using a 'reduce' operator
    * followed by 'flatMap'
    */
 
-   aggregation = algn.out
-                     .reduce([:]) { map, tuple ->    // 'map' is used to collect all values; 'tuple' is the record containing four items: barcode, seqid, bam file and bai file
-                         def barcode = tuple[0]      // the first item is the 'barcode'
-                         def group = map[barcode]    // get the aggregation for current 'barcode'
-                         if( !group ) group = [ barcode, [], [], [] ]    // if new, create a new entry
-                         group[1] << tuple[1]        // append 'seq_id' to the aggregation list
-                         group[2] << tuple[2]        // append 'bam' file to the aggregation list
-                         group[3] << tuple[3]        // append 'bai' file to the aggregation list
-                         map[barcode] = group        // set back into the map
-                         return map                  // return it so that it will be used in the next iteration
-                     }
-                     .flatMap { it.values() }        // tricky part: get the list of values of in the map, each value is the
-                                                     // aggregation build above
-                                                     // the 'flatMap' emits each of these aggregation list as a single item
-
-                     .map { it.collect {  it instanceof Collection ? it.sort() : it }   }
+  aggregation = align.out
+    // 'map' is used to collect all values; 'tuple' is the record containing four items: barcode, seqid, bam file and bai file
+    .reduce([:]) { map, tuple ->
+      def barcode = tuple[0]      // the first item is the 'barcode'
+      def group = map[barcode]    // get the aggregation for current 'barcode'
+      if( !group ) group = [ barcode, [], [], [] ]    // if new, create a new entry
+      group[1] << tuple[1]        // append 'seq_id' to the aggregation list
+      group[2] << tuple[2]        // append 'bam' file to the aggregation list
+      group[3] << tuple[3]        // append 'bai' file to the aggregation list
+      map[barcode] = group        // set back into the map
+      return map                  // return it so that it will be used in the next iteration
+    }
+
+    // tricky part: get the list of values of in the map, each value is the
+    // aggregation build above
+    // the 'flatMap' emits each of these aggregation list as a single item
+    .flatMap { map -> map.values() }
+    .map { group ->
+      group.collect { v -> v instanceof Collection ? v.sort() : v }
+    }
 
    merge(aggregation)
 }

tests/collect_tuple-dsl2.nf

@@ -13,6 +13,7 @@ process algn {
   output:
   tuple val(barcode), val(seq_id), path('bam'), path('bai')
 
+  script:
   """
   echo BAM $seq_id - $barcode > bam
   echo BAI $seq_id - $barcode > bai
@@ -30,6 +31,7 @@ process merge {
   input:
   tuple val(barcode), val(seq_id), path(bam, stageAs:'bam?'), path(bai, stageAs:'bai?')
 
+  script:
   """
   echo barcode: $barcode
   echo seq_ids: $seq_id

tests/complex-names-dsl2.nf

@@ -3,6 +3,7 @@
 process foo {
   publishDir 'foo', mode: 'copy'
   container 'debian:latest'
+
   output:
   path '*.fa'
   path 'hello.txt'
@@ -12,32 +13,33 @@ process foo {
   path '.alpha'
 
   script:
-  $/
+  '''
   echo A > hello.txt
   echo B > sample.zip 
   echo C > sample.html
-  echo D > 01_A\(R1\).fastq
-  echo E > 01_A\(R2\).fastq
-  echo F > sample_\(1\ 2\).vcf
+  echo D > 01_A\\(R1\\).fastq
+  echo E > 01_A\\(R2\\).fastq
+  echo F > sample_\\(1\\ 2\\).vcf
   echo 1 > f1.fa
   echo 2 > f2.fa
   echo 3 > f3.fa
   mkdir .alpha
   echo "Hello world!" > .alpha/hello.txt
-  /$
+  '''
 }
 
 process bar {
   debug true
   container 'debian:latest'
+
   input: 
   path '*'
 
   script:
-  $/
+  '''
   cat .alpha/hello.txt
   [ `cat * | grep -c ''` == 9 ] || false
-  /$
+  '''
 }
 
 /*

tests/config-labels.config

@@ -32,6 +32,6 @@ profiles {
     }
 
     test3 {
-        includeConfig 'config-labels.included'
+        includeConfig 'config-labels-included.config'
     }
 }