From 4807d76146fdfc7b6771eebb26ae879ceced6575 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 8 Apr 2019 15:51:14 +0200
Subject: [PATCH 1/2] add logging of ignored errored processes

---
 .../{{cookiecutter.name_noslash}}/main.nf                  | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
index a5e941f7c0..a3d90900ad 100644
--- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
+++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
@@ -366,6 +366,13 @@ workflow.onComplete {
     c_purple = params.monochrome_logs ? '' : "\033[0;35m";
     c_green = params.monochrome_logs ? '' : "\033[0;32m";
     c_red = params.monochrome_logs ? '' : "\033[0;31m";
+
+    if (workflow.stats.ignoredCountFmt > 0 && workflow.success) {
+      log.info "${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}"
+      log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
+      log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
+    }
+
     if(workflow.success){
         log.info "${c_purple}[{{ cookiecutter.name }}]${c_green} Pipeline completed successfully${c_reset}"
     } else {

From b8fa3dd4c1a65e42d14eb175c9ec8ba02df90f40 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Mon, 8 Apr 2019 15:57:17 +0200
Subject: [PATCH 2/2] update changelog

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4f985c44f2..b2bf65e111 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,8 @@
   * Improved documentation
 * Fixed bugs in `nf-core lint`
   * The order of conda channels is now correct, avoiding occasional erroneous errors that packages weren't found ([#207](https://github.com/nf-core/tools/issues/207))
+* Add reporting of ignored errored process
+  * As a solution for [#103](https://github.com/nf-core/tools/issues/103))
 
 ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark