From b45d56bad7e048bdaabaffec8fe81e0a3830f35a Mon Sep 17 00:00:00 2001
From: Jorrit Boekel <jorrit.boekel@scilifelab.se>
Date: Mon, 16 Mar 2020 15:10:44 +0100
Subject: [PATCH] In case of median sweep, output empty channelmedians table

---
 environment.yml | 2 +-
 main.nf         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index f3c26e0..8bf7444 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - bioconda::msgf_plus=2019.07.03
+  - bioconda::msgf_plus=2020.03.12
   - bioconda::hardklor=2.3.0
   - bioconda::kronik=2.20
   - bioconda::msstitch=2.19
diff --git a/main.nf b/main.nf
index faa54b6..da8a3f7 100644
--- a/main.nf
+++ b/main.nf
@@ -859,7 +859,7 @@ process normalizeFeaturesDEqMS {
   paste pepacc <(cut -f "\$channelcols" psms) > psmvals
   # run deqMS normalization and summarization, which produces logged ratios
 
-  ${params.denoms ? "denomcols=\$(egrep -n \'(${setdenoms[setname].join('|')})\' <( head -n1 psmvals | tr '\\t' '\\n') | cut -f1 -d ':' | tr '\\n' ',' | sed 's/,\$//') " : ""}
+  ${params.denoms ? "denomcols=\$(egrep -n \'(${setdenoms[setname].join('|')})\' <( head -n1 psmvals | tr '\\t' '\\n') | cut -f1 -d ':' | tr '\\n' ',' | sed 's/,\$//') " : "touch ${setname}_channelmedians"}
   deqms_normalize.R psmvals features $setname ${params.denoms ? "\$denomcols" : ''}
   # join feat tables on normalized proteins
   paste <(head -n1 features) <(head -n1 normalized_feats | cut -f2-2000) <(echo PSM counts) > ${setname}_feats