Merge pull request #55 from nf-core/dev

Release 1.2.6

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/mhcquant:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/mhcquant:dev nfcore/mhcquant:1.2.5
+  - docker tag nfcore/mhcquant:dev nfcore/mhcquant:1.2.6
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/mhcquant: Changelog
 
+## v1.2.6 nf-core/mhcquant "Golden Eagle" - 2019/03/05
+
+### `Fixed`
+linear retention time alignment
+refine_fdr README
+
 ## v1.2.5 nf-core/mhcquant "Golden Eagle" - 2019/02/26
 
 ### `Fixed`

Dockerfile

@@ -6,5 +6,5 @@ COPY environment.yml /
 COPY environment-percolator.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 RUN conda env create -f /environment-percolator.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-mhcquant-1.2.5/bin:$PATH
-ENV PATH /opt/conda/envs/nf-core-mhcquant-percolator-1.2.5/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mhcquant-1.2.6/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mhcquant-percolator-1.2.6/bin:$PATH

README.md

@@ -21,7 +21,7 @@ The pipeline is built using Nextflow, a workflow tool to run tasks across multip
 
 ### Run
 ```
-nextflow run nf-core/mhcquant --mzmls '*.mzML' --fasta 'SWISSPROT_12_2018.fasta' --alleles 'alleles.tsv' --vcf 'variants.vcf' --include_proteins_from_vcf --run_prediction -profile standard,docker
+nextflow run nf-core/mhcquant --mzmls '*.mzML' --fasta 'SWISSPROT_12_2018.fasta' --alleles 'alleles.tsv' --vcf 'variants.vcf' --include_proteins_from_vcf --run_prediction --refine_fdr_on_predicted_subset -profile standard,docker
 ```
 
 ### Documentation

Singularity

@@ -3,11 +3,11 @@ Bootstrap:docker
 
 %labels
     DESCRIPTION Singularity image containing all requirements for the nf-core/mhcquant pipeline
-    VERSION 1.2.5
+    VERSION 1.2.6
 
 %environment
-    PATH=/opt/conda/envs/nf-core-mhcquant-1.2.5/bin:$PATH
-    PATH=/opt/conda/envs/nf-core-mhcquant-percolator-1.2.5/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-mhcquant-1.2.6/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-mhcquant-percolator-1.2.6/bin:$PATH
     export PATH
 
 %files

docs/usage.md

@@ -33,6 +33,7 @@
     * [`--enzyme`](#--enzyme)
     * [`--fixed_mods`](#--fixed_mods)
     * [`--variable_mods`](#--variable_mods)
+    * [`--max_rt_alignment_shift`](#--max_rt_alignment_shift)
     * [`--spectrum_batch_size`](#--spectrum_batch_size)
 * [Optional binding predicion](#optional-binding-prediction)
     * [`--run_prediction`](#--run_prediction)
@@ -209,6 +210,9 @@ Specify which fixed modifications should be applied to the database search (eg.
 ### `--variable_mods`
 Specify which variable modifications should be applied to the database search (eg. 'Oxidation (M)', see OpenMS modifications)
 
+### `--max_rt_alignment_shift`
+Set a maximum retention time shift for the linear rt alignment
+
 ### `--spectrum_batch_size`
 Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)
 

environment-percolator.yml

@@ -1,4 +1,4 @@
-name: nf-core-mhcquant-percolator-1.2.5
+name: nf-core-mhcquant-percolator-1.2.6
 channels:
   - bioconda
   - conda-forge

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-mhcquant-1.2.5
+name: nf-core-mhcquant-1.2.6
 channels:
   - bioconda
   - conda-forge

main.nf

@@ -25,7 +25,7 @@ def helpMessage() {
 
     The typical command for running the pipeline is as follows:
 
-    nextflow run nf-core/mhcquant --mzmls '*.mzML' --fasta '*.fasta' --vcf '*.vcf' --alleles 'alleles.tsv' --include_proteins_from_vcf --run_prediction -profile standard,docker
+    nextflow run nf-core/mhcquant --mzmls '*.mzML' --fasta '*.fasta' --vcf '*.vcf' --alleles 'alleles.tsv' --include_proteins_from_vcf --run_prediction --refine_fdr_on_predicted_subset -profile standard,docker
 
     Mandatory arguments:
       --mzmls                           Path to input data (must be surrounded with quotes)
@@ -51,6 +51,7 @@ def helpMessage() {
       --run_centroidisation             Specify whether mzml data is peak picked or not (true, false)
       --pick_ms_levels                  The ms level used for peak picking (eg. 1, 2)
       --prec_charge                     Precursor charge (eg. "2:3")
+      --max_rt_alignment_shift          Maximal retention time shift (sec) resulting from linear alignment      
       --spectrum_batch_size             Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)
 
     Binding Predictions:
@@ -509,7 +510,7 @@ process filter_fdr_for_idalignment {
      IDFilter -in ${id_file_idx_fdr} \\
               -out ${id_file_idx_fdr.baseName}_filtered.idXML \\
               -threads ${task.cpus} \\
-              -score:pep 0.05  \\
+              -score:pep 0.05 \\
               -remove_decoys
      """
 
@@ -531,7 +532,9 @@ process align_ids {
      def out_names = id_names.collect { it.baseName+'.trafoXML' }.join(' ')
      """
      MapAlignerIdentification -in $id_names \\
-                              -trafo_out $out_names
+                              -trafo_out $out_names \\
+                              -model:type linear \\
+                              -algorithm:max_rt_shift ${params.max_rt_alignment_shift}
      """
 
 }

nextflow.config

@@ -11,7 +11,7 @@
 // Global default params, used in configs
 params {
 
-  container = 'nfcore/mhcquant:1.2.5' // Container slug. Stable releases should specify release tag!
+  container = 'nfcore/mhcquant:1.2.6' // Container slug. Stable releases should specify release tag!
 
   help = false
   mzmls = "data/*.mzML"
@@ -47,6 +47,7 @@ params {
   activation_method = 'ALL'
   enzyme = 'unspecific cleavage'
   fixed_mods = ''
+  max_rt_alignment_shift = 300
   spectrum_batch_size = 500
   variable_mods = 'Oxidation (M)'
   tracedir = "${params.outdir}/pipeline_info"
@@ -123,7 +124,7 @@ manifest {
   description = 'Identify and quantify peptides from mass spectrometry raw data'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'
-  version = '1.2.5'
+  version = '1.2.6'
 }
 
 // Function to ensure that resource requirements don't go beyond