Bug fixes, spacing and variable initialisation

CHANGELOG.md

@@ -54,6 +54,10 @@
 * Plain-text email template now has nf-core ASCII artwork
 * Template configured to use logo fetched from website
 * New option `--email_on_fail` which only sends emails if the workflow is not successful
+* Add file existence check when checking software versions
+* Fixed issue [https://github.com/nf-core/tools/issues/165] - Use `checkIfExists`
+* Consistent spacing for `if` statements
+* Add sensible resource labels to `base.config`
 
 ### Other
 

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/assets/email_template.txt

@@ -1,9 +1,9 @@
 ----------------------------------------------------
-                                          ,--./,-.
-          ___     __   __   __   ___     /,-._.--~\
-    |\ | |__  __ /  ` /  \ |__) |__         }  {
-    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
-                                          `._,._,'
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
   {{ cookiecutter.name }} v${version}
 ----------------------------------------------------
 

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/bin/scrape_software_versions.py

@@ -18,11 +18,14 @@
 
 # Search each file using its regex
 for k, v in regexes.items():
-    with open(v[0]) as x:
-        versions = x.read()
-        match = re.search(v[1], versions)
-        if match:
-            results[k] = "v{}".format(match.group(1))
+    try:
+        with open(v[0]) as x:
+            versions = x.read()
+            match = re.search(v[1], versions)
+            if match:
+                results[k] = "v{}".format(match.group(1))
+    except IOError:
+        results[k] = False
 
 # Remove software set to false in results
 for k in results:

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/base.config

@@ -13,16 +13,40 @@ process {
 
   // TODO nf-core: Check the defaults for all processes
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
   time = { check_max( 4.h * task.attempt, 'time' ) }
 
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 1
   maxErrors = '-1'
 
   // Process-specific resource requirements
+  // NOTE - Only one of the labels below are used in the fastqc process in the main script.
+  //        If possible, it would be nice to keep the same label naming convention when
+  //        adding in your processes.
   // TODO nf-core: Customise requirements for specific processes.
   // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+  withLabel:process_low {
+    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
+    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
+    time = { check_max( 6.h * task.attempt, 'time' ) }
+  }
+  withLabel:process_medium {
+    cpus = { check_max( 6 * task.attempt, 'cpus' ) }
+    memory = { check_max( 42.GB * task.attempt, 'memory' ) }
+    time = { check_max( 8.h * task.attempt, 'time' ) }
+  }
+  withLabel:process_high {
+    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
+    memory = { check_max( 84.GB * task.attempt, 'memory' ) }
+    time = { check_max( 10.h * task.attempt, 'time' ) }
+  }
+  withLabel:process_long {
+    time = { check_max( 20.h * task.attempt, 'time' ) }
+  }
+  withName:get_software_versions {
+    cache = false
+  }
 }
 
 params {

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/test.config

@@ -14,6 +14,7 @@ params {
   max_cpus = 2
   max_memory = 6.GB
   max_time = 48.h
+
   // Input data
   // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
   // TODO nf-core: Give any required params for the test so that command line flags are not needed