Merge pull request #44 from Leon-Bichmann/master

1.2.4

.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:1.2.3
+  - docker tag nfcore/mhcquant:dev nfcore/mhcquant:1.2.4
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -1,5 +1,10 @@
 # nf-core/mhcquant: Changelog
 
+## v1.2.4 nf-core/mhcquant "Golden Eagle" - 2019/02/02
+
+### `Fixed`
+fixed refine_fdr_on_predicted_subset float error
+
 ## v1.2.3 nf-core/mhcquant "Golden Eagle" - 2019/02/02
 
 ### `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-1.2.3/bin:$PATH
-ENV PATH /opt/conda/envs/nf-core-mhcquant-percolator-1.2.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mhcquant-1.2.4/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-mhcquant-percolator-1.2.4/bin:$PATH

Singularity

@@ -3,11 +3,11 @@ Bootstrap:docker
 
 %labels
     DESCRIPTION Singularity image containing all requirements for the nf-core/mhcquant pipeline
-    VERSION 1.2.3
+    VERSION 1.2.4
 
 %environment
-    PATH=/opt/conda/envs/nf-core-mhcquant-1.2.3/bin:$PATH
-    PATH=/opt/conda/envs/nf-core-mhcquant-percolator-1.2.3/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-mhcquant-1.2.4/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-mhcquant-percolator-1.2.4/bin:$PATH
     export PATH
 
 %files

bin/mhcflurry_predict_mztab_for_filtering.py

@@ -34,7 +34,7 @@
    print allele
    predictor = Class1AffinityPredictor.load()
    df_pred=predictor.predict_to_dataframe(allele=allele, peptides=seqs_new_greater_qval)
-   seqs_filtered+=df_pred[df_pred['prediction']<=sys.argv[-5]]['peptide'].values.tolist()
+   seqs_filtered+=df_pred[df_pred['prediction']<=float(sys.argv[-5])]['peptide'].values.tolist()
 
 #merge sequence lists and append decoys
 seqs_new_all=list(set(seqs_new_smaller_qval+seqs_filtered))

environment-percolator.yml

@@ -1,4 +1,4 @@
-name: nf-core-mhcquant-percolator-1.2.3
+name: nf-core-mhcquant-percolator-1.2.4
 channels:
   - bioconda
   - conda-forge

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-mhcquant-1.2.3
+name: nf-core-mhcquant-1.2.4
 channels:
   - bioconda
   - conda-forge

main.nf

@@ -713,6 +713,7 @@ process filter_by_q_value_first {
  * STEP 12.1 - option refine_fdr_on_predicted_subset: export filtered percolator results as mztab
  */
 process export_mztab_perc {
+    publishDir "${params.outdir}/Intermediate_Results/"
 
     input:
      file percolator_mztab from id_files_merged_psm_perc_filtered_refine
@@ -737,6 +738,7 @@ process export_mztab_perc {
  * STEP 12.2 - option refine_fdr_on_predicted_subset: export psm results as mztab
  */
 process export_mztab_psm {
+    publishDir "${params.outdir}/Intermediate_Results/"
 
     input:
      file psm_mztab from id_files_merged_psm_refine

nextflow.config

@@ -11,7 +11,7 @@
 // Global default params, used in configs
 params {
 
-  container = 'nfcore/mhcquant:1.2.3' // Container slug. Stable releases should specify release tag!
+  container = 'nfcore/mhcquant:1.2.4' // Container slug. Stable releases should specify release tag!
 
   help = false
   mzmls = "data/*.mzML"
@@ -123,7 +123,7 @@ manifest {
   description = 'Identify and quantify peptides from mass spectrometry raw data'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'
-  version = '1.2.3'
+  version = '1.2.4'
 }
 
 // Function to ensure that resource requirements don't go beyond