Merge pull request #217 from nf-core/dev

Prepare for release 2.3.1
nf-core · May 10, 2022 · bc0a2dd · bc0a2dd
2 parents b24db1e + 83c79fa
commit bc0a2dd
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,20 @@
 # nf-core/mhcquant: Changelog
 
+## v2.3.1 nfcore/mhcquant "White Gold Swallow" - 2022/05/10
+
+### `Added`
+
+- [#210](https://github.com/nf-core/mhcquant/pull/210) - Icons to the different parameters in the `nextflow_schema.json`
+
+### `Fixed`
+
+- [#211](https://github.com/nf-core/mhcquant/issues/211) Resolved the problem that there was no output from `OPENMS_MZTABEXPORTER_QUANT`
+- [#212](https://github.com/nf-core/mhcquant/issues/212) - Altered the CometAdapter functionalities for resolve the issue with the `fixed_mods`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v2.3.0 nfcore/mhcquant "White Gold Swallow" - 2022/04/05
 
 ### `Added`

diff --git a/conf/modules.config b/conf/modules.config
@@ -134,10 +134,18 @@ process {
             ]
         }
 
-    withName: 'OPENMS_DECOYDATABASE|OPENMS_THERMORAWFILEPARSER|OPENMS_PEAKPICKERHIRES|OPENMS_PEPTIDEINDEXER|OPENMS_FALSEDISCOVERYRATE|OPENMS_IDMERGER|OPENMS_MAPRTTRANSFORMER.*ML|OPENMS_FEATURE.*|OPENMS_IDCONFLICTRESOLVER|OPENMS_MZTABEXPORTER' {
+    withName: 'OPENMS_DECOYDATABASE|OPENMS_THERMORAWFILEPARSER|OPENMS_PEAKPICKERHIRES|OPENMS_PEPTIDEINDEXER|OPENMS_FALSEDISCOVERYRATE|OPENMS_IDMERGER|OPENMS_MAPRTTRANSFORMER.*ML|OPENMS_FEATURE.*|OPENMS_IDCONFLICTRESOLVER' {
             publishDir       = [ enabled: false ]
         }
 
+    withName: 'OPENMS_MZTABEXPORTER_QUANT' {
+            publishDir  = [
+                path: { "${params.outdir}/Intermediate_Results" },
+                mode: params.publish_dir_mode,
+                pattern: '*.mzTab'
+            ]
+    }
+
     withName: 'OPENMS_TEXTEXPORTER_UNQUANTIFIED|OPENMS_TEXTEXPORTER_QUANTIFIED' {
             ext.args    = [
                 "-id:add_metavalues 0"

diff --git a/modules/local/openms_cometadapter.nf b/modules/local/openms_cometadapter.nf
@@ -18,7 +18,7 @@ process OPENMS_COMETADAPTER {
         def prefix           = task.ext.prefix ?: "${mzml.baseName}"
         def args             = task.ext.args  ?: ''
 
-        def mods             = params.fixed_mods != " " ? "-fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")}" : ""
+        def mods             = params.fixed_mods != " " ? "-fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")}" : "-fixed_modifications"
         def xions            = params.use_x_ions ? "-use_X_ions true" : ""
         def zions            = params.use_z_ions ? "-use_Z_ions true" : ""
         def aions            = params.use_a_ions ? "-use_A_ions true" : ""

diff --git a/nextflow.config b/nextflow.config
@@ -204,7 +204,7 @@ manifest {
     description     = 'Identify and quantify peptides from mass spectrometry raw data'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version = '2.3.0'
+    version = '2.3.1'
 }
 
 // Function to ensure that resource requirements don't go beyond