Update process snippets to comply with strict syntax (#5526) [ci skip]

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

docs/cache-and-resume.md

@@ -148,6 +148,8 @@ process gather {
     input:
     tuple val(id), file(foo)
     tuple val(id), file(bar)
+
+    script:
     """
     merge_command $foo $bar
     """
@@ -168,6 +170,8 @@ workflow {
 process gather {
     input:
     tuple val(id), file(foo), file(bar)
+
+    script:
     """
     merge_command $foo $bar
     """

docs/channel.md

@@ -45,6 +45,7 @@ process foo {
   output:
   path 'x.txt'
 
+  script:
   """
   echo $x > x.txt
   """

docs/conda.md

@@ -49,9 +49,10 @@ Conda package names can specified using the `conda` directive. Multiple package
 process foo {
   conda 'bwa samtools multiqc'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 
@@ -98,9 +99,10 @@ The path of an environment file can be specified using the `conda` directive:
 process foo {
   conda '/some/path/my-env.yaml'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 
@@ -128,9 +130,10 @@ If you already have a local Conda environment, you can use it in your workflow s
 process foo {
   conda '/path/to/an/existing/env/directory'
 
-  '''
+  script:
+  """
   your_command --here
-  '''
+  """
 }
 ```
 

docs/container.md

@@ -293,17 +293,19 @@ It is possible to specify a different Docker image for each process definition i
 process foo {
   container 'image_name_1'
 
-  '''
+  script:
+  """
   do this
-  '''
+  """
 }
 
 process bar {
   container 'image_name_2'
 
-  '''
+  script:
+  """
   do that
-  '''
+  """
 }
 ```
 
@@ -380,17 +382,19 @@ It is possible to specify a different container image for each process definitio
 process foo {
   container 'image_name_1'
 
-  '''
+  script:
+  """
   do this
-  '''
+  """
 }
 
 process bar {
   container 'image_name_2'
 
-  '''
+  script:
+  """
   do that
-  '''
+  """
 }
 ```
 

docs/developer/nextflow.ast.md

@@ -32,6 +32,7 @@ process splitLetters {
   output:
     path 'chunk_*'
 
+  script:
   """
   printf '${params.str}' | split -b 6 - chunk_
   """
@@ -43,6 +44,7 @@ process convertToUpper {
   output:
     stdout
 
+  script:
   """
   cat $x | tr '[a-z]' '[A-Z]'
   """
@@ -62,6 +64,7 @@ process( splitLetters( {
   output:
     path('chunk_*')
 
+  script:
   """
   printf '${params.str}' | split -b 6 - chunk_
   """
@@ -73,6 +76,7 @@ process( convertToUpper( {
   output:
     stdout
 
+  script:
   """
   cat $x | tr '[a-z]' '[A-Z]'
   """

docs/developer/plugins.md

@@ -141,6 +141,8 @@ You can then use this executor in your pipeline:
 ```nextflow
 process foo {
     executor 'my-executor'
+
+    // ...
 }
 ```
 

docs/dsl1.md

@@ -29,6 +29,7 @@ process splitLetters {
     output:
     file 'chunk_*' into letters
 
+    script:
     """
     printf '${params.str}' | split -b 6 - chunk_
     """
@@ -41,6 +42,7 @@ process convertToUpper {
     output:
     stdout result
 
+    script:
     """
     cat $x | tr '[a-z]' '[A-Z]'
     """

docs/google.md

@@ -104,6 +104,7 @@ process myTask {
     cpus 8
     memory '40 GB'
 
+    script:
     """
     your_command --here
     """
@@ -112,6 +113,7 @@ process myTask {
 process anotherTask {
     machineType 'n1-highmem-8'
 
+    script:
     """
     your_command --here
     """
@@ -130,6 +132,7 @@ process myTask {
     memory '20 GB'
     machineType 'n2-*,c2-*,m3-*'
 
+    script:
     """
     your_command --here
     """
@@ -148,6 +151,7 @@ process myTask {
     memory '20 GB'
     machineType 'template://my-template'
 
+    script:
     """
     your_command --here
     """
@@ -341,16 +345,18 @@ process custom_resources_task {
     memory '40 GB'
     disk '200 GB'
 
+    script:
     """
-    <Your script here>
+    your_command --here
     """
 }
 
 process predefined_resources_task {
     machineType 'n1-highmem-8'
 
+    script:
     """
-    <Your script here>
+    your_command --here
     """
 }
 ```

docs/metrics.md

@@ -21,6 +21,7 @@ In the first example, let's consider the simple use case in which a process perf
 process CpuUsageEx1 {
   cpus 2
 
+  script:
   """
   stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
   """
@@ -35,6 +36,7 @@ In the second example, some time will be spent performing pure computation and s
 process CpuUsageEx2 {
   cpus 1
 
+  script:
   """
   stress -c 1 -t 10 # compute square-root of random numbers during 10s using 1 CPU
   stress -c 1 -t 5 # compute square-root of random numbers during 5s using 1 CPU
@@ -57,6 +59,7 @@ The third example is similar to the second one except that the pure computation
 process CpuUsageEx3 {
   cpus 2
 
+  script:
   """
   stress -c 2 -t 10 # compute square-root of random numbers during 10s using 2 CPUs
   sleep 10 # use no CPU during 10s
@@ -232,6 +235,7 @@ The first and second programs are executed in `foo` and `bar` processes respecti
 process foo {
     memory '1.5 GB'
 
+    script:
     """
     memory_vmem_1GiB_ram_0Gib
     """
@@ -240,6 +244,7 @@ process foo {
 process bar {
     memory '1.5 GB'
 
+    script:
     """
     memory_vmem_1GiB_ram_1Gib
     """

docs/overview.md

@@ -33,6 +33,7 @@ process blastSearch {
   output:
   path "top_hits.txt"
 
+  script:
   """
   blastp -db $db -query $query -outfmt 6 > blast_result
   cat blast_result | head -n 10 | cut -f 2 > top_hits.txt
@@ -47,6 +48,7 @@ process extractTopHits {
   output:
   path "sequences.txt"
 
+  script:
   """
   blastdbcmd -db $db -entry_batch $top_hits > sequences.txt
   """