Add in possibility for netMHCpan via path

README.md

@@ -38,7 +38,6 @@ nextflow run nf-core/epitopeprediction -profile test,<docker/singularity/conda/i
 
 iv. Start running your own analysis!
 
-<!-- TODO nf-core: Update the default command above used to run the pipeline -->
 ```bash
 nextflow run nf-core/epitopeprediction -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37
 ```

conf/base.config

@@ -23,7 +23,6 @@ process {
   // NOTE - Only one of the labels below are used in the fastqc process in the main script.
   //        If possible, it would be nice to keep the same label naming convention when
   //        adding in your processes.
-  // TODO nf-core: Customise requirements for specific processes.
   // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
   withLabel:process_low {
     cpus = { check_max( 2 * task.attempt, 'cpus' ) }

docs/usage.md

@@ -15,6 +15,7 @@
   * [Reference genomes](#reference-genomes)
     * [`--genome` (using iGenomes)](#genome-using-igenomes)
     * [`--fasta`](#fasta)
+    * [`--netmhcpan`](#netmhcpan)
     * [`--igenomes_ignore`](#igenomesignore)
   * [Job resources](#job-resources)
     * [Automatic resubmission](#automatic-resubmission)
@@ -178,6 +179,10 @@ If you prefer, you can specify the full path to your reference genome when you r
 --fasta '[path to Fasta reference]'
 ```
 
+### `--netmhcpan`
+
+Configure path to exported [netMHCpan](https://services.healthtech.dtu.dk/service.php?NetMHCIIpan) directory. The directory should already contain the required data for netMHCPan that needs to be installed by the user separately. 
+
 ### `--igenomes_ignore`
 
 Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.

environment.yml

@@ -7,8 +7,8 @@ dependencies:
   - python=2.7.15 #dont upgrade, FRED2 needs python 2.7 for now
   - multiqc=1.6 #cant upgrade due to Python2 fix
   - snpsift=4.3.1t
-  - csvtk=0.17.0
-  - fred2=2.0.3
-  - mhcflurry=1.2.4
+  - csvtk=0.19.1
+  - fred2=2.0.4
+  - mhcflurry=1.4.3
   - mhcnuggets=2.2
-  - conda-forge::r-markdown=0.9
+  - conda-forge::r-markdown=1.1

main.nf

@@ -31,11 +31,12 @@ def helpMessage() {
     Alternative inputs:
       --peptides                    Path to TSV file containing peptide sequences (minimum required: id and sequence column)
     
-    Options:
+    Pipeline options:
       --filter_self                 Specifies that peptides should be filtered against the specified human proteome references Default: false
       --wild_type                   Specifies that wild-type sequences of mutated peptides should be predicted as well Default: false
       --mhc_class                   Specifies whether the predictions should be done for MHC class I or class II. Default: 1
       --peptide_length              Specifies the maximum peptide length Default: MHC class I: 8 to 11 AA, MHC class II: 15 to 16 AA 
+      --netmhcpan                   Specifies the path to netMHCPan installation 
 
     References                      If not specified in the configuration file or you wish to overwrite any of the references
       --reference_genome            Specifies the ensembl reference genome version (GRCh37, GRCh38) Default: GRCh37
@@ -90,6 +91,9 @@ params.reference_proteome = false
 multiqc_config = file(params.multiqc_config)
 output_docs = file("$baseDir/docs/output.md")
 
+//Check if netmhcpan needs to be used
+if (params.netmhcpan) netmhcpan_path = file(params.netmhcpan)
+
 ch_split_peptides = Channel.empty()
 ch_split_variants = Channel.empty()
 
@@ -130,11 +134,6 @@ if ( params.filter_self & !params.reference_proteome ){
     params.reference_proteome = file("$baseDir/assets/")
 }
 
-// AWSBatch sanity checking
-if(workflow.profile == 'awsbatch'){
-    if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
-    if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!"
-}
 //
 // NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
 // If you want to use the channel below in a process, define the following:
@@ -250,6 +249,30 @@ process get_software_versions {
     """
 }
 
+
+/*
+* Prepare netmhcpan installation for running on HPC clusters properly
+*/
+
+process prepare_netmhcpan{
+
+    input:
+    file netmhcpan_path from netmhcpan_path
+
+    when: params.netmhcpan
+
+    output:
+    file(netmhcpan_path) into netmhcpan_path_for_fred2
+
+    script:
+    """
+    #Fix path to netMHCPan correctly
+    sed -i "s#setenv  NMHOME.*#setenv  NMHOME  ${netmhcpan_path}" ${netmhcpan_path}/netMHCpan
+    #Fix tmp folder to /tmp for clusters
+    sed -i "s#setenv  TMPDIR.*#setenv  TMPDIR   /tmp" ${netmhcpan_path}/netMHCpan
+    """
+}
+
 /*
  * STEP 1 - Split variant data
  */