Merge branch 'dev' into generate_speclib

nf-core · Jan 22, 2025 · 4f65a3d · 4f65a3d
2 parents c40fcb7 + e2a6509
commit 4f65a3d
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Showing 29 changed files with 920 additions and 213 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added global fdr evaluation in new local subworkflow `RESCORE` [#338](https://github.com/nf-core/mhcquant/pull/338)
 - Added `-weights` parameter in `OPENMS_PERCOLATORADAPTER` and visualize the median feature weights in multiQC report [#347](https://github.com/nf-core/mhcquant/pull/347)
 - Added flag `generate_speclib` that will generate a spectrum library for DIA searches with EasyPQP [#349](https://github.com/nf-core/mhcquant/pull/349)
+- Replace local with nf-core modules [#350](https://github.com/nf-core/mhcquant/pull/347)
 
 ### `Fixed`
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -62,6 +62,14 @@ process {
         ]
     }
 
+    withName: 'OPENMS_FILEFILTER' {
+        ext.prefix  = {"${file.baseName}_filtered"}
+        ext.args    = "-peak_options:rm_pc_charge 0"
+        publishDir  = [
+            enabled: false
+        ]
+    }
+
     withName: 'OPENMS_DECOYDATABASE' {
         ext.args    = [
             "-decoy_string DECOY_",
@@ -81,6 +89,51 @@ process {
         ]
     }
 
+    withName: 'OPENMSTHIRDPARTY_COMETADAPTER' {
+        ext.prefix  = {"${mzml.baseName}"}
+        ext.args    = { [
+            (params.default_params_file_comet != " ") ? "-default_params_file ${params.default_params_file_comet}" : "",
+            "-pin_out ${mzml.baseName}_pin.tsv",
+            "-instrument ${params.instrument}",
+            "-spectrum_batch_size ${params.spectrum_batch_size}",
+            "-activation_method ${params.activation_method}",
+            "-precursor_mass_tolerance ${params.precursor_mass_tolerance}",
+            "-precursor_error_units ${params.precursor_error_units}",
+            "-fragment_mass_tolerance ${params.fragment_mass_tolerance}",
+            "-fragment_bin_offset ${params.fragment_bin_offset}",
+            "-num_hits ${params.num_hits}",
+            "-digest_mass_range ${params.digest_mass_range}",
+            "-max_variable_mods_in_peptide ${params.number_mods}",
+            "-missed_cleavages 0",
+            "-precursor_charge ${params.prec_charge}",
+            "-fixed_modifications ${params.fixed_mods.tokenize(',').collect {"'${it}'"}.join(" ")}",
+            "-variable_modifications ${params.variable_mods.tokenize(',').collect {"'${it}'"}.join(" ")}",
+            "-enzyme '${params.enzyme}'",
+            "-use_X_ions ${params.use_x_ions}",
+            "-use_Z_ions ${params.use_z_ions}",
+            "-use_A_ions ${params.use_a_ions}",
+            "-use_C_ions ${params.use_c_ions}",
+            "-use_NL_ions ${params.use_NL_ions}",
+            params.remove_precursor_peak ? "-remove_precursor_peak yes" : "",
+        ].join(' ').trim() }
+        publishDir = [
+            path: {"${params.outdir}/intermediate_results/comet"},
+            mode: params.publish_dir_mode,
+            pattern: '*.tsv'
+        ]
+    }
+
+    withName: 'OPENMS_PEPTIDEINDEXER' {
+        ext.prefix  = {"${meta.id}_idx"}
+        ext.args = [
+                "-decoy_string DECOY",
+                "-enzyme:specificity none"
+                ].join(' ').trim()
+        publishDir  = [
+            enabled: false
+        ]
+    }
+
     withName: 'OPENMS_IDMERGER|OPENMS_IDMERGER_QUANT' {
         ext.args    = [
             "-annotate_file_origin true",
@@ -246,12 +299,6 @@ process {
         ]
     }
 
-    withName: 'OPENMS_FILEFILTER' {
-        publishDir  = [
-            enabled: false
-        ]
-    }
-
     withName: 'PYOPENMS_CHROMATOGRAMEXTRACTOR' {
         publishDir  = [
             enabled: false
@@ -277,36 +324,6 @@ process {
         ]
     }
 
-    withName: 'OPENMS_COMETADAPTER' {
-        ext.args    = [
-            "-precursor_mass_tolerance ${params.precursor_mass_tolerance}",
-            "-precursor_error_units ${params.precursor_error_units}",
-            "-fragment_mass_tolerance ${params.fragment_mass_tolerance}",
-            "-fragment_bin_offset ${params.fragment_bin_offset}",
-            "-instrument ${params.instrument}",
-            "-num_hits ${params.num_hits}",
-            "-digest_mass_range ${params.digest_mass_range}",
-            "-max_variable_mods_in_peptide ${params.number_mods}",
-            "-missed_cleavages 0",
-            "-precursor_charge ${params.prec_charge}",
-            "-activation_method ${params.activation_method}",
-            "-variable_modifications ${params.variable_mods.tokenize(',').collect {"'${it}'"}.join(" ")}",
-            "-enzyme '${params.enzyme}'",
-            "-spectrum_batch_size ${params.spectrum_batch_size}"
-        ].join(' ').trim()
-        publishDir = [
-            path: {"${params.outdir}/intermediate_results/comet"},
-            mode: params.publish_dir_mode,
-            pattern: '*.tsv'
-        ]
-    }
-
-    withName: 'OPENMS_PEPTIDEINDEXER' {
-        publishDir  = [
-            enabled: false
-        ]
-    }
-
     withName: 'OPENMS_IDMASSACCURACY' {
         ext.prefix  = {"${meta.spectra}"}
         ext.args    = [

diff --git a/modules.json b/modules.json
@@ -20,6 +20,11 @@
                         "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
+                    "openms/filefilter": {
+                        "branch": "master",
+                        "git_sha": "26a34ecd378f06094eb253615932d8cc634474cb",
+                        "installed_by": ["modules"]
+                    },
                     "openms/idfilter": {
                         "branch": "master",
                         "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
@@ -50,6 +55,16 @@
                         "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
+                    "openms/peptideindexer": {
+                        "branch": "master",
+                        "git_sha": "573ba82ecf1505775d1a4332bc3cf55cacc3d094",
+                        "installed_by": ["modules"]
+                    },
+                    "openmsthirdparty/cometadapter": {
+                        "branch": "master",
+                        "git_sha": "573ba82ecf1505775d1a4332bc3cf55cacc3d094",
+                        "installed_by": ["modules"]
+                    },
                     "thermorawfileparser": {
                         "branch": "master",
                         "git_sha": "2d0e53d398315b4e8ed06e81c175dc05d90f33d5",

diff --git a/modules/local/openms_cometadapter.nf b/modules/local/openms_cometadapter.nf
diff --git a/modules/local/openms_filefilter.nf b/modules/local/openms_filefilter.nf
diff --git a/modules/local/openms_peptideindexer.nf b/modules/local/openms_peptideindexer.nf
diff --git a/modules/nf-core/openms/filefilter/environment.yml b/modules/nf-core/openms/filefilter/environment.yml
diff --git a/modules/nf-core/openms/filefilter/main.nf b/modules/nf-core/openms/filefilter/main.nf