Merge pull request #473 from atrigila/deseq_formula

Add formula to `DESEQ2`

Author: atrigila

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [[#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)).
 - [[#441](https://github.com/nf-core/differentialabundance/pull/441)] - Add dream differential module. ([@nschcolnicov](https://github.com/nschcolnicov) and [@alanmmobbs93](https://github.com/alanmobbs93), review by [@pinin4fjords](https://github.com/pinin4fjords), [@suzannejin](https://github.com/suzannejin) and [@grst](https://github.com/grst)).

conf/modules.config

@@ -267,6 +267,7 @@ process {
             "--vst_nsub $meta.params.deseq2_vst_nsub",
             "--shrink_lfc $meta.params.deseq2_shrink_lfc",
             "--cores $meta.params.deseq2_cores",
+            "--seed $meta.params.deseq2_seed",
             "--subset_to_contrast_samples $meta.params.differential_subset_to_contrast_samples",
             ((meta.params.round_digits != null && meta.params.round_digits > 0) ? "--round_digits $meta.params.round_digits" : ""),
             ((meta.blocking == null) ? '' : "--blocking_variables $meta.blocking")

docs/usage.md

@@ -200,10 +200,7 @@ contrasts:
 The necessary fields in order are:
 
 - `formula` - A string representation of the model formula. It is used to build the design matrix.
-- `make_contrasts_str` - An explicit literal contrast string (e.g., "treatmenthND6 - treatmentmCherry") that is passed directly to [`limma::makeContrasts()`](https://rdrr.io/bioc/limma/man/makeContrasts.html) in `VARIANCEPARTITION_DREAM` and `LIMMA_DIFFERENTIAL`. The parameter names must be syntactically valid variable names in R (see [`make.names`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/make.names.html)). This field provides full control for complex designs. Requires `formula`.
-
-> [!WARNING]
-> Formula-based contrasts are currently only supported by `VARIANCEPARTITION_DREAM` and `LIMMA_DIFFERENTIAL`. They **do not work** with tools like `DESEQ2` yet.
+- `make_contrasts_str` - An explicit literal contrast string (e.g., "treatmenthND6 - treatmentmCherry") that is passed directly to [`limma::makeContrasts()`](https://rdrr.io/bioc/limma/man/makeContrasts.html) in `VARIANCEPARTITION_DREAM`, `LIMMA_DIFFERENTIAL` and `DESEQ2_DIFFERENTIAL`. The parameter names must be syntactically valid variable names in R (see [`make.names`](https://stat.ethz.ch/R-manual/R-devel/library/base/html/make.names.html)). This field provides full control for complex designs. Requires `formula`.
 
 > [!NOTE]
 >
@@ -223,7 +220,6 @@ Beyond the basic one-factor comparison, the YAML contrasts format supports advan
 contrasts:
   - id: genotype_WT_KO_treatment_Control_Treated
     formula: "~ genotype * treatment"
-    comparison: ["genotype", "WT", "KO"]
     make_contrasts_str: "genotypeKO.treatmentTreated"
 ```
 

modules.json

@@ -17,7 +17,7 @@
                     },
                     "custom/filterdifferentialtable": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "custom/matrixfilter": {
@@ -42,7 +42,7 @@
                     },
                     "deseq2/differential": {
                         "branch": "master",
-                        "git_sha": "25c228dd132d91596e87b636b0e03fd48d4c951a",
+                        "git_sha": "2e24bf8b6b045e1cf56a2907306b008113a686d0",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "geoquery/getgeo": {
@@ -72,7 +72,7 @@
                     },
                     "limma/differential": {
                         "branch": "master",
-                        "git_sha": "41d1a6ad16756e12a424e508cbe3a1b3b8639946",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "propr/grea": {
@@ -82,7 +82,7 @@
                     },
                     "propr/propd": {
                         "branch": "master",
-                        "git_sha": "ce6e8e8bc0c00d284733d7c48ddc794873f60ffe",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "proteus/readproteingroups": {
@@ -122,7 +122,7 @@
                     },
                     "variancepartition/dream": {
                         "branch": "master",
-                        "git_sha": "c48c4b3d11fb243c888235d1e6b18d6c5059b2bb",
+                        "git_sha": "73b1b0fc276e2a6bd753e4d3d10d754b72a3e345",
                         "installed_by": ["abundance_differential_filter"]
                     },
                     "zip": {
@@ -136,7 +136,7 @@
                 "nf-core": {
                     "abundance_differential_filter": {
                         "branch": "master",
-                        "git_sha": "4006954b7bfbbc61c7d5fb009319ed536d2ffca4",
+                        "git_sha": "2e24bf8b6b045e1cf56a2907306b008113a686d0",
                         "installed_by": ["subworkflows"]
                     },
                     "differential_functional_enrichment": {