Merge pull request #498 from nf-core/dedup-gc-overhead-fix

Dedup gc overhead fix

Author: jfy133

conf/base.config

@@ -95,9 +95,15 @@ process {
     errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' } 
   }
 
+  // other process specific exit statuses
+  withName: nuclear_contamination {
+    errorStrategy = { task.exitStatus in [134] ? 'ignore' : 'retry' }
+  }
+
   withName: multiqc {
     errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
+
 }
 
 params {

main.nf

@@ -584,7 +584,6 @@ if (params.input && (has_extension(params.input, "tsv"))) tsv_path = params.inpu
 ch_input_sample = Channel.empty()
 if (tsv_path) {
 
-
     tsv_file = file(tsv_path)
     if (!tsv_file.exists()) exit 1, "[nf-core/eager] error: input TSV file could not be found. Does the file exist or in the right place? You gave the path: ${params.input}"
 
@@ -2608,9 +2607,6 @@ process sex_deterrmine {
     tag "${samplename}"
     publishDir "${params.outdir}/nuclear_contamination", mode:"copy"
 
-    // ANGSD Xcontamination will exit with status 134 when the number of SNPs is too low
-    validExitStatus 0,134
-
     when:
     params.run_nuclear_contamination
 
@@ -3057,11 +3053,13 @@ workflow.onComplete {
             log.info "[nf-core/eager] Sent summary e-mail to $email_address (sendmail)"
         } catch (all) {
             // Catch failures and try with plaintext
-              def mail_cmd = [ 'mail', '-s', subject, '--content-type=text', email_address ]
-              if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
+            def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+            if (mqc_report == NULL) {
+                log.warn "[nf-core/eager] Could not attach MultiQC report to summary email"
+            } else if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) {
                 mail_cmd += [ '-A', mqc_report ]
             }
-            mail_cmd.execute() << email_txt 
+            mail_cmd.execute() << email_html 
             log.info "[nf-core/eager] Sent summary e-mail to $email_address (mail)"
         }
     }