added workflow.onComplete/onError snippet, updated init and illumina …

…snippets

README.md

@@ -23,3 +23,4 @@ Nextflow syntax highlighting extends Sublime Text 3's Groovy syntax with highlig
 - `cpus`: insert "${task.cpus}" into a script
 - `script_path`: specify user script (e.g. Python script) to use from `scripts/` directory in workflow base directory
 - `info`: `log.info` snippet 
+- `done`: on workflow complete or error message

messages/install.txt

@@ -20,6 +20,7 @@ Snippets:
 - cpus: insert "${task.cpus}" into a script
 - script_path: specify user script (e.g. Python script) to use from scripts/ directory in workflow base directory
 - info: log.info snippet 
+- done: on workflow complete or error message
 
 
 Nextflow syntax highlighting extends Sublime Text 3's Groovy syntax with highlighting of: 

nextflow-done-log-oncomplete-onerror.sublime-snippet

@@ -0,0 +1,22 @@
+<snippet>
+    <content><![CDATA[
+workflow.onComplete {
+    println """
+    Pipeline execution summary
+    ---------------------------
+    Completed at : \${workflow.complete}
+    Duration     : \${workflow.duration}
+    Success      : \${workflow.success}
+    Results Dir  : \${file(params.outdir)}
+    Work Dir     : \${workflow.workDir}
+    Exit status  : \${workflow.exitStatus}
+    Error report : \${workflow.errorReport ?: '-'}
+    """.stripIndent()
+}
+workflow.onError {
+    println "Oops... Pipeline execution stopped with the following message: \${workflow.errorMessage}"
+}
+]]></content>
+    <tabTrigger>done</tabTrigger>
+    <scope>source.nextflow - meta.definition.process.nextflow</scope>
+</snippet>

nextflow-init.sublime-snippet

@@ -3,8 +3,7 @@
 #!/usr/bin/env nextflow
 
 params.outdir = "\$baseDir/results"
-params.$1 = $2
-params.$3 = $4
+params.${1:reads} = ${2:"\$baseDir/reads/*R{1,2\}*.fastq.gz"}
 
 outdir = params.outdir
 
@@ -21,7 +20,6 @@ def helpMessage() {
     nextflow run ${workflow.manifest.name} -profile standard --outdir /output/path
     Options:
       --$1                          Help message for "$1" (default: $2)
-      --$3                          Help message for "$3" (default: $4)
     Other options:
       --outdir                      The output directory where the results will be saved (default: \$outdir)
       -w/--work-dir                 The temporary directory where intermediate data will be saved

nextflow-paired-end-illumina-reads-input-channel.sublime-snippet

@@ -3,7 +3,7 @@
 Channel
   .fromFilePairs( ${1:params.reads}, ${2:flat: true})
   .map { [ it[0].replaceAll(/_S\d{1,2}_L001/, ""), it[1], it[2] ] }
-  .set { ${3:samples_ch} }
+  .set { ${3:ch_reads} }
 ]]></content>
 	<tabTrigger>illumina</tabTrigger>
 	<scope>source.nextflow - meta.definition.process.nextflow</scope>