Matrixfilter NA options

CHANGELOG.md

@@ -7,16 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [[#244](https://github.com/nf-core/differentialabundance/pull/244)] - Add pipeline params for matrixfilter NA options ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#241](https://github.com/nf-core/differentialabundance/pull/241)] - Template update for nf-core/tools v2.13 ([@WackerO](https://github.com/WackerO), review by [@nvnieuwk](https://github.com/nvnieuwk))
 - [[#228](https://github.com/nf-core/differentialabundance/pull/228)] - Template update for nf-core/tools v2.12 ([@nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords), [@WackerO](https://github.com/WackerO))
 - [[#222](https://github.com/nf-core/differentialabundance/pull/222)] - Add rounding to all numeric report tables ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#219](https://github.com/nf-core/differentialabundance/pull/219)] - Template update for nf-core/tools v2.11.1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#197](https://github.com/nf-core/differentialabundance/pull/197)] - Add contributor info to report ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 
 ### `Fixed`
 
-- [[#231](https://github.com/nf-core/differentialabundance/pull/231) - Update GSEA module to fix butterfly plot bug ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#226](https://github.com/nf-core/differentialabundance/pull/226) - Fix DESEQ2_NORM in modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
-- [[#221](https://github.com/nf-core/differentialabundance/pull/221) - Update shinyngs modules to address density plots issue ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
+- [[#231](https://github.com/nf-core/differentialabundance/pull/231)] - Update GSEA module to fix butterfly plot bug ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#226](https://github.com/nf-core/differentialabundance/pull/226)] - Fix DESEQ2_NORM in modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
+- [[#221](https://github.com/nf-core/differentialabundance/pull/221)] - Update shinyngs modules to address density plots issue ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [[#223](https://github.com/nf-core/differentialabundance/pull/223)] - tabulartogseacls fixes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse))
 - [[#213](https://github.com/nf-core/differentialabundance/pull/213)] - Fix volcano plot legend ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#210](https://github.com/nf-core/differentialabundance/pull/210)] - Include Affy timeout fix ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
@@ -139,7 +141,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0.1 - 2023-01-25
 
-- [[#49](https://github.com/nf-core/differentialabundance/pull/49) - Add citation fixes, missing logos, output detail, and trigger Zenodo ([@pinin4fjords](https://github.com/pinin4fjords), review by [@apeltzer](https://github.com/apeltzer), [@jfy133](https://github.com/jfy133))
+- [[#49](https://github.com/nf-core/differentialabundance/pull/49)] - Add citation fixes, missing logos, output detail, and trigger Zenodo ([@pinin4fjords](https://github.com/pinin4fjords), review by [@apeltzer](https://github.com/apeltzer), [@jfy133](https://github.com/jfy133))
 
 ## v1.0.0 - 2023-01-23
 

conf/modules.config

@@ -464,7 +464,9 @@ process {
             "--minimum_samples ${params.filtering_min_samples}",
             "--minimum_abundance ${params.filtering_min_abundance}",
             (params.filtering_min_proportion ? "--minimum_proportion ${params.filtering_min_proportion}" : ''),
-            (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : '')
+            (params.filtering_grouping_var ? "--grouping_variable \"${params.filtering_grouping_var}\"" : ''),
+            (params.filtering_min_proportion_not_na ? "--minimum_proportion_not_na \"${params.filtering_min_proportion_not_na}\"" : ''),
+            (params.filtering_min_samples_not_na ? "--minimum_samples_not_na \"${params.filtering_min_samples_not_na}\"" : '')
         ].join(' ').trim()
     }
 

nextflow.config

@@ -70,10 +70,12 @@ params {
     proteus_palette_name      = 'Set1'
 
     // Filtering options
-    filtering_min_samples      = 1.0
-    filtering_min_abundance    = 1.0
-    filtering_min_proportion   = null
-    filtering_grouping_var     = null
+    filtering_min_samples           = 1.0
+    filtering_min_abundance         = 1.0
+    filtering_min_proportion        = null
+    filtering_grouping_var          = null
+    filtering_min_proportion_not_na = 0.5
+    filtering_min_samples_not_na    = null
 
     // Exploratory options
     exploratory_main_variable      = 'auto_pca'

nextflow_schema.json

@@ -329,6 +329,17 @@
                     "help_text": "The variable can be used to define groups and derive a minimum group size upon which to base minimum observation numbers. The rationale for this is to allow retention of features that might be present in only one group. Note that this is consciously NOT filtering with an explicit awareness of groups (\"feature must be present in all samples of group A\"), since this is known to create biases towards discovery of differential features.",
                     "description": "An optional grouping variable to be used to calculate a min_samples value",
                     "fa_icon": "fas fa-users"
+                },
+                "filtering_min_proportion_not_na": {
+                    "type": "number",
+                    "default": 0.5,
+                    "description": "A minimum proportion of observations, given as a number between 0 and 1, that must have a value (not NA) to retain the row/ feature (e.g. gene).",
+                    "fa_icon": "fas fa-compress-alt"
+                },
+                "filtering_min_samples_not_na": {
+                    "type": "number",
+                    "description": "Minimum observations that must have a value (not NA) to retain the row/ feature (e.g. gene). Overrides filtering_min_proportion_not_na.",
+                    "fa_icon": "fas fa-percent"
                 }
             },
             "fa_icon": "fas fa-filter",