Merge pull request #517 from atrigila/expose_dream_params

Author: atrigila

CHANGELOG.md

@@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [[#517](https://github.com/nf-core/differentialabundance/pull/473)] - Expose DREAM options as pipeline params. ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).
 -[[#510]](https://github.com/nf-core/differentialabundance/pull/510) - Add decoupler module to differential functional enrichment subworkflow. ([@antoniasaracco](https://github.com/antoniasaracco), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).
-
 - [[#473](https://github.com/nf-core/differentialabundance/pull/473)] - Allow formula-based contrasts in DESEQ2. ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst)).
 - [[#443](https://github.com/nf-core/differentialabundance/pull/443)] - Add toolsheet-related implementations. ([@suzannejin](https://github.com/suzannejin), review by [@pinin4fjords](https://github.com/pinin4fjords), [@mirpedrol](https://github.com/mirpedrol) and [@JoseEspinosa](https://github.com/JoseEspinosa))
 - [[#450](https://github.com/nf-core/differentialabundance/pull/441)] - Allow usage of strings for makeContrasts in DREAM. ([@atrigila](https://github.com/atrigila), review by [@pinin4fjords](https://github.com/pinin4fjords), [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst)).

conf/modules.config

@@ -356,6 +356,21 @@ process {
                 pattern: '*.dream.results.tsv'
             ]
         ]
+        ext.args = { [
+            "--adjust.method ${meta.params.dream_adjust_method}",
+            "--p.value ${meta.params.dream_p_value}",
+            "--lfc ${meta.params.dream_lfc}",
+            "--confint ${meta.params.dream_confint}",
+            "--proportion ${meta.params.dream_proportion}",
+            "--stdev_coef_lim ${meta.params.dream_stdev_coef_lim}",
+            "--trend ${meta.params.dream_trend}",
+            "--robust ${meta.params.dream_robust}",
+            "--winsor_tail_p ${meta.params.dream_winsor_tail_p}",
+            "--ddf ${meta.params.dream_ddf}",
+            "--reml ${meta.params.dream_reml}",
+            "--apply_voom ${meta.params.dream_apply_voom}",
+            ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking")
+        ].join(' ').trim() }
     }
 
     withName: CUSTOM_FILTERDIFFERENTIALTABLE {

modules.json

@@ -127,7 +127,7 @@
                     },
                     "variancepartition/dream": {
                         "branch": "master",
-                        "git_sha": "73b1b0fc276e2a6bd753e4d3d10d754b72a3e345",
+                        "git_sha": "342edbcb60c7e59db0d5c3f8bb64dbb2d9d62785",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "zip": {

modules/nf-core/variancepartition/dream/templates/dream.R

@@ -138,6 +138,20 @@ params {
     limma_confint           = false
     limma_use_voom          = false
 
+    // DREAM-specific options
+    dream_adjust_method     = "BH"
+    dream_p_value           = 1
+    dream_lfc               = 0
+    dream_confint           = false
+    dream_proportion        = 0.01
+    dream_stdev_coef_lim    = '0.1,4'
+    dream_trend             = false
+    dream_robust            = false
+    dream_winsor_tail_p     = '0.05,0.1'
+    dream_ddf               = 'adaptive'
+    dream_reml              = false
+    dream_apply_voom        = false
+
     // IMMUNEDECONV options
     immunedeconv_run        = false
     immunedeconv_method     = "quantiseq" // Other options can be found in https://omnideconv.org/immunedeconv/articles/immunedeconv.html

nextflow.config

@@ -356,13 +356,13 @@
             "properties": {
                 "filtering_min_abundance": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "description": "Minimum abundance value",
                     "fa_icon": "fas fa-compress-alt"
                 },
                 "filtering_min_samples": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "description": "Minimum observations that must pass the threshold to retain the row/ feature (e.g. gene).",
                     "fa_icon": "fas fa-compress-alt"
                 },
@@ -541,13 +541,13 @@
                 },
                 "differential_min_fold_change": {
                     "type": "number",
-                    "default": 2.0,
+                    "default": 2,
                     "description": "Minimum fold change used to calculate differential feature numbers",
                     "fa_icon": "fas fa-angle-double-down"
                 },
                 "differential_max_pval": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "description": "Maximum p value used to calculate differential feature numbers",
                     "fa_icon": "fas fa-angle-double-up"
                 },
@@ -805,7 +805,7 @@
                 },
                 "limma_p_value": {
                     "type": "number",
-                    "default": 1.0,
+                    "default": 1,
                     "description": "cutoff value for adjusted p-values. Only genes with lower p-values are listed.",
                     "fa_icon": "fas fa-angle-double-up"
                 },
@@ -817,6 +817,57 @@
             },
             "fa_icon": "fas fa-border-all"
         },
+        "differential_dream_specific_options": {
+            "title": "[differential] DREAM specific options",
+            "type": "object",
+            "description": "",
+            "default": "",
+            "properties": {
+                "dream_p_value": {
+                    "type": "integer",
+                    "default": 1
+                },
+                "dream_lfc": {
+                    "type": "integer",
+                    "default": 0
+                },
+                "dream_confint": {
+                    "type": "boolean"
+                },
+                "dream_proportion": {
+                    "type": "number",
+                    "default": 0.01
+                },
+                "dream_stdev_coef_lim": {
+                    "type": "string",
+                    "default": "0.1,4"
+                },
+                "dream_trend": {
+                    "type": "boolean"
+                },
+                "dream_robust": {
+                    "type": "boolean"
+                },
+                "dream_winsor_tail_p": {
+                    "type": "string",
+                    "default": "0.05,0.1"
+                },
+                "dream_ddf": {
+                    "type": "string",
+                    "default": "adaptive"
+                },
+                "dream_reml": {
+                    "type": "boolean"
+                },
+                "dream_apply_voom": {
+                    "type": "boolean"
+                },
+                "dream_adjust_method": {
+                    "type": "string",
+                    "default": "BH"
+                }
+            }
+        },
         "functional_functional_analysis_options": {
             "title": "[functional] Functional analysis options",
             "type": "object",
@@ -1369,6 +1420,9 @@
         {
             "$ref": "#/$defs/differential_limma_specific_options"
         },
+        {
+            "$ref": "#/$defs/differential_dream_specific_options"
+        },
         {
             "$ref": "#/$defs/functional_functional_analysis_options"
         },