Fix all stuff mentioned by Maxime

skrakau · Dec 5, 2019 · 755a2f0 · 755a2f0
1 parent a9a5101
commit 755a2f0
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/conf/test.config b/conf/test.config
@@ -13,6 +13,6 @@ params {
   max_time = 48.h
 
   // Input data
-  somatic_mutations = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/variants/variants.vcf'
+  input = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/variants/variants.vcf'
   alleles = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/alleles/alleles.txt'
 }
diff --git a/conf/test_variant_tsv.config b/conf/test_variant_tsv.config
@@ -13,6 +13,6 @@ params {
   max_time = 48.h
 
   // Input data
-  somatic_mutations = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/variants/variants.tsv'
+  input = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/variants/variants.tsv'
   alleles = 'https://github.com/nf-core/test-datasets/raw/epitopeprediction/testdata/alleles/alleles.txt'
 }
diff --git a/docs/usage.md b/docs/usage.md
@@ -19,7 +19,7 @@
   * [`--mhc_class`](#mhcclass)
   * [`--min_peptide_length`](#minpeptidelength)
   * [`--max_peptide_length``](#maxpeptidelength)
-    * [`--genome`](#genome)
+  * [`--genome`](#genome)
   * [`--proteome`](#proteome)
   * [`--tools`](#tools)
   * [`--wild_type`](#wildtype)
@@ -144,7 +144,7 @@ Specifies the minimum peptide length. By default, for MHC Class I this is 8 amin
 Specifies the maximum peptide length. By default, for MHC Class I this is 11 amino acids. For MHC Class II this is by default 16
 amino acids.
 
-### `--genome`
+## `--genome`
 
 This defines against which reference genome the pipeline performs the analysis. The default choice is `GRCh37`, as most clinical labs still rely on `GRCh37` as the human reference genome to use. Available are `GRCh37` and `GRCh38`.
 

diff --git a/main.nf b/main.nf
@@ -20,10 +20,10 @@ def helpMessage() {
 
     The typical command for running the pipeline is as follows:
 
-    nextflow run nf-core/epitopeprediction -profile <docker/singularity/conda/institute> --somatic_mutations "*.vcf.gz" --genome GRCh37
+    nextflow run nf-core/epitopeprediction -profile <docker/singularity/conda/institute> --input "*.vcf.gz"
 
     Mandatory arguments:
-      --somatic_mutations           Path to input data (must be surrounded with quotes)
+      --input           Path to input data (must be surrounded with quotes)
       --alleles                     Path to the file containing the MHC alleles
       -profile                      Configuration profile to use. Can use multiple (comma separated)
                                     Available: conda, docker, singularity, awsbatch, test and more
@@ -35,13 +35,13 @@ def helpMessage() {
       --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
-      --max_peptide_length              Specifies the maximum peptide length Default: MHC class I: 11 aa, MHC class II: 16 aa 
+      --max_peptide_length          Specifies the maximum peptide length Default: MHC class I: 11 aa, MHC class II: 16 aa 
       --min_peptide_length          Specifies the minimum peptide length Default: MCH class I: 8 aa, MHC class II: 15 aa
       --tools                       Specifies a list of tool(s) to use. Available are: 'syfpeithi', 'mhcflurry', 'mhcnuggets-class-1', 'mhcnuggets-class-2'. Can be combined in a list separated by comma.
 
     References                      If not specified in the configuration file or you wish to overwrite any of the references
       --genome                      Specifies the ensembl reference genome version (GRCh37, GRCh38) Default: GRCh37
-      --proteome          Specifies the reference proteome(s) used for self-filtering
+      --proteome                    Specifies the reference proteome(s) used for self-filtering
        
     Other options:
       --outdir                      The output directory where the results will be saved
@@ -283,7 +283,7 @@ process peptidePrediction {
    file "*.json" into ch_json_reports
 
    script:
-   def input_type = params.peptides ? "--peptides ${inputs}" : "--somatic_mutations ${inputs}"
+   def input_type = params.peptides ? "--peptides ${inputs}" : "--input ${inputs}"
    def ref_prot = params.proteome ? "--proteome ${params.proteome}" : ""
    def wt = params.wild_type ? "--wild_type" : ""
    """

diff --git a/nextflow.config b/nextflow.config
@@ -16,7 +16,7 @@ params {
   min_peptide_length = (mhc_class == 1) ? 8 : 15
   tools = 'syfpeithi'
   genome = 'GRCh37'
-  somatic_mutations = false
+  input = false
   wild_type = false
 
   // Additional annotation files