From 9512bb070f5b83b0c7640878bb732f007da166b6 Mon Sep 17 00:00:00 2001
From: Jorrit Boekel <jorrit.boekel@scilifelab.se>
Date: Fri, 16 Sep 2022 14:59:35 +0200
Subject: [PATCH] Version update to 2.11, added some parameter documentation as
 well

---
 CHANGELOG.md    | 5 +++++
 Dockerfile      | 2 +-
 Singularity     | 4 ++--
 environment.yml | 2 +-
 main.nf         | 6 ++++++
 nextflow.config | 4 ++--
 6 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a3a8fcc..1905731 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,9 @@
 # lehtiolab/ddamsproteomics: Changelog
+## Version 2.11 [2022-09-16]
+- Bugfix in MS1 quant where too large retention time tolerance was used
+- MS1 quant RT/mz tolerances parametrized
+
+
 ## Version 2.10 [2022-09-02]
 - Bugfix to allow setnames with spaces etc (quoting)
 - Dynamic memory allocation for MSGF
diff --git a/Dockerfile b/Dockerfile
index 6afc221..32173a5 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,4 +5,4 @@ RUN apt update && apt install -y fontconfig && apt clean -y
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/ddamsproteomics-2.10/bin:$PATH
+ENV PATH /opt/conda/envs/ddamsproteomics-2.11/bin:$PATH
diff --git a/Singularity b/Singularity
index 7a28bbb..e57aa91 100644
--- a/Singularity
+++ b/Singularity
@@ -3,10 +3,10 @@ Bootstrap:docker
 
 %labels
     DESCRIPTION Singularity image containing all requirements for the lehtiolab/ddamsproteomics pipeline
-    VERSION 2.10
+    VERSION 2.11
 
 %environment
-    PATH=/opt/conda/envs/ddamsproteomics-2.10/bin:$PATH
+    PATH=/opt/conda/envs/ddamsproteomics-2.11/bin:$PATH
     export PATH
 
 %files
diff --git a/environment.yml b/environment.yml
index 47bdbae..4d9c0ba 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: ddamsproteomics-2.10
+name: ddamsproteomics-2.11
 channels:
   - bioconda
   - conda-forge
diff --git a/main.nf b/main.nf
index 8d9d1de..f779247 100644
--- a/main.nf
+++ b/main.nf
@@ -80,6 +80,10 @@ def helpMessage() {
                                     window) for assigning isobaric quant to PSMs. PSMs below this value
                                     get assigned NA. A number between 0 and 1. Default 0 allows all PSMs
                                     quant values.
+      --ms1qrttol                   Tolerance window for retention time in seconds (backwards and forwards)
+                                    to align MS1 areas (from dinosaur, hardklor/kronik) to MS2 scans
+      --ms1qmztol                   Tolerance window for m/z in ppm (plus and minus) to align MS1 areas found within 
+                                    the RT tolerance window.
       --normalize                   Normalize isobaric values by median centering on channels of protein table
       --sampletable                 Path to sample annotation table in case of isobaric analysis
       --deqms                       Perform DEqMS differential expression analysis using sampletable
@@ -323,6 +327,8 @@ summary['Peptide FDR cutoff'] = params.pepconflvl
 summary['Isobaric label sets/denominators'] = params.isobaric
 summary['Isobaric quant: activation method'] = params.activation
 summary['Isobaric PSM minimum precursor purity'] = params.minprecursorpurity
+summary['Retention time tolerance for MS1 alignment'] = params.ms1qrttol
+summary['m/z tolerance for MS1 alignment'] = params.ms1qmztol
 summary['Keep PSMs for quant with NA in any channel'] = params.keepnapsmsquant
 summary['Explicit isobaric normalization'] = params.normalize
 summary['Perform DE analysis (implies normalization)'] = params.deqms
diff --git a/nextflow.config b/nextflow.config
index 25e3bbe..deeeeac 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,7 +20,7 @@ params {
 }
 
 // Container slug. Stable releases should specify release tag!
-process.container = 'lehtiolab/ddamsproteomics:2.10'
+process.container = 'lehtiolab/ddamsproteomics:2.11'
 //process.container = 'ddamsproteomics:dev'
 
 profiles {
@@ -89,7 +89,7 @@ manifest {
   description = 'Quantitative DDA MS proteomics pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'
-  version = '2.10'
+  version = '2.11'
 }
 
 // Function to ensure that resource requirements don't go beyond