From 6c70d65ae6c59a78fdc13072a114bfa530325b0a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Patrick=20H=C3=BCther?= <patrick.huether@gmail.com>
Date: Tue, 6 Apr 2021 11:59:00 +0200
Subject: [PATCH] bismark/report: allow missing input data (#400)

* bismark/report: allow missing data

* bismark/summary: improve matching of process output
---
 software/bismark/report/main.nf  | 10 +++-------
 software/bismark/summary/main.nf |  4 ++--
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/software/bismark/report/main.nf b/software/bismark/report/main.nf
index 68db2e19..574e0ffb 100644
--- a/software/bismark/report/main.nf
+++ b/software/bismark/report/main.nf
@@ -22,17 +22,13 @@ process BISMARK_REPORT {
     tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias)
 
     output:
-    tuple val(meta), path("*{html,txt}"), emit: report
-    path  "*.version.txt"               , emit: version
+    tuple val(meta), path("*report.{html,txt}"), emit: report
+    path  "*.version.txt"                      , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     """
-    bismark2report \\
-        --alignment_report $align_report \\
-        --dedup_report $dedup_report \\
-        --splitting_report $splitting_report \\
-        --mbias_report $mbias
+    bismark2report $options.args
 
     echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
     """
diff --git a/software/bismark/summary/main.nf b/software/bismark/summary/main.nf
index d61ad2d7..8cb23be6 100644
--- a/software/bismark/summary/main.nf
+++ b/software/bismark/summary/main.nf
@@ -25,8 +25,8 @@ process BISMARK_SUMMARY {
     path(mbias)
 
     output:
-    path("*{html,txt}")  , emit: summary
-    path  "*.version.txt", emit: version
+    path  "*report.{html,txt}", emit: summary
+    path  "*.version.txt"     , emit: version
 
     script:
     def software = getSoftwareName(task.process)