Merge pull request #152 from nf-core/dev

Update trigger for AWS megatests

.github/workflows/awsfulltest.yml

@@ -1,10 +1,14 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on push to the master branch.
+# This workflow is triggered after release after the nf-core Docker push workflow finished.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  workflow_run:
+    workflows: ["nf-core Docker push"]
+    branches: [master]
+    types: 
+      - completed
+  workflow_dispatch:
 
 jobs:
   run-awstest:

.github/workflows/awstest.yml

@@ -3,9 +3,7 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch
 
 on:
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   run-awstest:

CHANGELOG.md

@@ -5,11 +5,15 @@
 ### `Added`
 
 - Template raise to 1.10.2
-- Added parameter scheme
-- Added real size AWS test profile
+- Added parameter json schema
+- Added full size AWS test profile
+- Included new parameters for Neutral loss and precursor ion inclusion
+
 
 ### `Fixed`
 
+- Changed trigger for AWS tests
+
 ### `Dependencies`
 
 ### `Deprecated`

main.nf

@@ -35,6 +35,8 @@ def helpMessage() {
       --use_z_ions [bool]                       Use z ions for spectral matching in addition
       --use_a_ions [bool]                       Use a ions for spectral matching in addition
       --use_c_ions [bool]                       Use c ions for spectral matching in addition
+      --use_NL_ions [bool]                      Use NL ions for spectral matching in addition
+      --remove_precursor_peak [bool]            Remove the precursor peak from the MS2 spectra
       --fdr_threshold [int]                     Threshold for FDR filtering
       --fdr_level [str]                         Level of FDR calculation ('peptide-level-fdrs', 'psm-level-fdrs', 'protein-level-fdrs')
       --digest_mass_range [int]                 Mass range of peptides considered for matching
@@ -187,6 +189,10 @@ params.use_a_ions = false
 a_ions = params.use_a_ions ? '-use_A_ions true' : ''
 params.use_c_ions = false
 c_ions = params.use_c_ions ? '-use_C_ions true' : ''
+params.use_NL_ions = false
+NL_ions = params.use_NL_ions ? '-use_NL_ions true' : ''
+params.remove_precursor_peak = false
+rm_precursor = params.remove_precursor_peak ? '-remove_precursor_peak true' : ''
 
 params.skip_decoy_generation = false
 if (params.skip_decoy_generation) {
@@ -581,15 +587,16 @@ process db_search_comet {
                    -allowed_missed_cleavages 0 \\
                    -precursor_charge ${params.prec_charge} \\
                    -activation_method ${params.activation_method} \\
-                   -use_NL_ions true \\
                    -variable_modifications ${params.variable_mods.tokenize(',').collect { "'${it}'" }.join(" ") } \\
                    -fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")} \\
                    -enzyme '${params.enzyme}' \\
                    -spectrum_batch_size ${params.spectrum_batch_size} \\
                    $a_ions \\
                    $c_ions \\
                    $x_ions \\
-                   $z_ions \\     
+                   $z_ions \\
+                   $NL_ions \\
+                   $rm_precursor \\
      """
 
 }

nextflow.config

@@ -75,6 +75,8 @@ params {
   use_z_ions = false
   use_a_ions = false
   use_c_ions = false
+  use_NL_ions = false
+  remove_precursor_peak = false
   skip_quantification = false
   quantification_fdr = false
 

nextflow_schema.json

@@ -181,6 +181,15 @@
                     "type": "boolean",
                     "description": "Include c ions into the peptide spectrum matching"
                 },
+                "use_NL_ions": {
+                    "type": "boolean",
+                    "description": "Include NL ions into the peptide spectrum matching"
+                },
+                "remove_precursor_peak": {
+                    "type": "boolean",
+                    "description": "Include precursor ions into the peptide spectrum matching",
+                    "default": true
+                },
                 "spectrum_batch_size": {
                     "type": "integer",
                     "default": 500,