reverting paramsheet to profiles

CHANGELOG.md

@@ -61,6 +61,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [[#644](https://github.com/nf-core/differentialabundance/pull/644)] - Reverted back to use profiles by default, and use paramsheet only when provided, ([@suzannejin](https://github.com/suzannejin)), review by [@pinin4fjords](https://github.com/pinin4fjords) and [@grst](https://github.com/grst).
 - [[#652](https://github.com/nf-core/differentialabundance/pull/652)] - Harmonize `--contrasts` and `--contrasts_yml` ([@atrigila](https://github.com/atrigila), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#626](https://github.com/nf-core/differentialabundance/pull/626)] - Update documentation, bump Nextflow version, `versions.yml` output cleanup and add params_yaml to report bundle ([@delfiterradas](https://github.com/delfiterradas), review by [@atrigila](https://github.com/atrigila), [@apeltzer](https://github.com/apeltzer), [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).
 - [[#628](https://github.com/nf-core/differentialabundance/pull/628)] - Removed `--deseq2_cores` parameter and infer from task cpus instead,([@delfiterradas](https://github.com/delfiterradas), review by [@grst](https://github.com/grst) and [@pinin4fjords](https://github.com/pinin4fjords)).

README.md

@@ -41,84 +41,80 @@ On release, automated continuous integration tests run the pipeline on a full-si
 8. Build an HTML report based on Quarto markdown, with interactive plots (where possible) and tables.
 
 > [!NOTE]
-> Each of these steps can be looped over multiple parameter sets, through paramsheet files and the `--paramset_name` parameter. See the [usage documentation](https://nf-co.re/differentialabundance/usage) for more information.
+> The pipeline supports two modes: **single-run mode** using analysis profiles (e.g. `-profile rnaseq,docker`) for production use, and **multi-run mode** using a custom paramsheet (`--paramsheet`) for comparing multiple configurations in parallel. See the [usage documentation](https://nf-co.re/differentialabundance/usage) for more information.
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-The paramsheet file (ie. `paramsheet.yaml`) stored in the `conf` directory defines the combination of tools and parameters that make sense to run for a given study type. You can use the flag `--paramset_name` to specify which set of tools to run. For example:
+Select an **analysis profile** that bundles the correct study type, differential method, and output settings. Combine it with a container profile (e.g. `docker`, `singularity`).
 
-RNA-seq with deseq2:
+RNA-seq with DESeq2 (default):
 
 ```bash
- nextflow run nf-core/differentialabundance \
-     --input samplesheet.csv \
-     --contrasts contrasts.yaml \
-     --matrix assay_matrix.tsv \
-     --gtf mouse.gtf \
-     --outdir <OUTDIR>  \
-     -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
-     --paramset_name deseq2_rnaseq
+nextflow run nf-core/differentialabundance \
+    -profile rnaseq,docker \
+    --input samplesheet.csv \
+    --contrasts contrasts.yaml \
+    --matrix assay_matrix.tsv \
+    --gtf mouse.gtf \
+    --outdir <OUTDIR>
 ```
 
-:::note
-If you are using the outputs of the nf-core rnaseq workflow as input here **either**:
-
-- supply the raw count matrices (file names like **gene_counts.tsv**) alongide the feature length matrix via `--feature_length_matrix` (rnaseq versions >=3.12.0, preferred)
-- **or** supply the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices.
+> [!NOTE]
+> If you are using the outputs of the nf-core rnaseq workflow as input here **either**:
+>
+> - supply the raw count matrices (file names like **gene_counts.tsv**) alongside the feature length matrix via `--feature_length_matrix` (rnaseq versions >=3.12.0, preferred)
+> - **or** supply the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices.
 
-RNA-seq limma+voom:
+RNA-seq with Limma (voom):
 
 ```bash
- nextflow run nf-core/differentialabundance \
-     --input samplesheet.csv \
-     --contrasts contrasts.yaml \
-     --matrix assay_matrix.tsv \
-     --gtf mouse.gtf \
-     --outdir <OUTDIR>  \
-     -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
-     --paramset_name limma_rnaseq
+nextflow run nf-core/differentialabundance \
+    -profile rnaseq_limma,docker \
+    --input samplesheet.csv \
+    --contrasts contrasts.yaml \
+    --matrix assay_matrix.tsv \
+    --gtf mouse.gtf \
+    --outdir <OUTDIR>
 ```
 
-:::note
-If you are using the outputs of the nf-core rnaseq workflow as input here you should provide either the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices. This follows the [recommendation from the tximport documentation](https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#limma-voom):
-
+> [!NOTE]
+> If you are using the outputs of the nf-core rnaseq workflow as input here you should provide either the **gene_counts_length_scaled.tsv** or **gene_counts_scaled.tsv** matrices. This follows the [recommendation from the tximport documentation](https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html#limma-voom):
+>
 > "Because limma-voom does not use the offset matrix stored in `y$offset`, we recommend using scaled counts generated from abundances, either 'scaledTPM' or 'lengthScaledTPM'."
 
-See the [usage documentation](https://nf-co.re/differentialabundance/usage) for more information.
-:::
+RNA-seq with DESeq2 and GSEA:
+
+```bash
+nextflow run nf-core/differentialabundance \
+    -profile rnaseq_deseq2_gsea,docker \
+    --input samplesheet.csv \
+    --contrasts contrasts.yaml \
+    --matrix assay_matrix.tsv \
+    --gtf mouse.gtf \
+    --gene_sets_files gene_sets.gmt \
+    --outdir <OUTDIR>
+```
 
 Affymetrix microarray:
 
 ```bash
- nextflow run nf-core/differentialabundance \
-     --input samplesheet.csv \
-     --contrasts contrasts.yaml \
-     --affy_cel_files_archive cel_files.tar \
-     --outdir <OUTDIR>  \
-     -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
-     --paramset_name limma_affy
+nextflow run nf-core/differentialabundance \
+    -profile affy,docker \
+    --input samplesheet.csv \
+    --contrasts contrasts.yaml \
+    --affy_cel_files_archive cel_files.tar \
+    --outdir <OUTDIR>
 ```
 
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
-RNA-seq with deseq2 and GSEA:
-
-```bash
- nextflow run nf-core/differentialabundance \
-     --input samplesheet.csv \
-     --contrasts contrasts.yaml \
-     --matrix assay_matrix.tsv \
-     --gtf mouse.gtf \
-     --outdir <OUTDIR>  \
-     -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
-     --paramset_name deseq2_rnaseq_gsea
-```
+Available analysis profiles: `rnaseq`, `rnaseq_deseq2_gsea`, `rnaseq_deseq2_gprofiler2`, `rnaseq_limma`, `rnaseq_limma_gsea`, `rnaseq_limma_gprofiler2`, `rnaseq_limma_decoupler`, `rnaseq_dream`, `rnaseq_dream_decoupler`, `affy`, `affy_limma_gsea`, `affy_limma_gprofiler2`, `maxquant`, `soft`. CLI flags override profile parameters following standard Nextflow precedence.
 
-You could also provide your own paramsheet through the `--paramsheet` parameter.
+For benchmarking multiple configurations in parallel, you can provide a custom paramsheet via `--paramsheet`. See the [usage documentation](https://nf-co.re/differentialabundance/usage) for more details on the multi-run mode.
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/differentialabundance/usage) and the [parameter documentation](https://nf-co.re/differentialabundance/parameters).
 

conf/affy/affy.config

@@ -0,0 +1,41 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Affymetrix microarray analysis profile (default: Limma)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Sets parameters for Affymetrix array differential abundance analysis using Limma.
+    Use as follows:
+        nextflow run nf-core/differentialabundance -profile affy,<docker/singularity> --input <SAMPLESHEET> --affy_cel_files_archive <TAR> --outdir <OUTDIR>
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    paramset_name                    = 'affy'
+
+    // Study
+    study_type                       = 'affy_array'
+    study_abundance_type             = 'intensities'
+
+    // Differential analysis (Limma)
+    differential_method              = 'limma'
+
+    // Features
+    features_id_col                  = 'PROBEID'
+    features_metadata_cols           = 'PROBEID,ENSEMBL,SYMBOL,GENETYPE'
+    features_name_col                = 'SYMBOL'
+    differential_feature_id_column   = 'PROBEID'
+    differential_feature_name_column = 'SYMBOL'
+
+    // Exploratory
+    exploratory_assay_names          = 'raw,normalised'
+    exploratory_final_assay          = 'normalised'
+    exploratory_log2_assays          = null
+
+    // Differential output columns
+    differential_file_suffix         = '.limma.results.tsv'
+    differential_fc_column           = 'logFC'
+    differential_pval_column         = 'P.Value'
+    differential_qval_column         = 'adj.P.Val'
+
+    // Shiny app
+    shinyngs_build_app               = true
+}

conf/affy/affy_limma_gprofiler2.config

@@ -0,0 +1,14 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Affymetrix Limma + g:Profiler2 analysis profile
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Inherits from affy.config and adds g:Profiler2 functional enrichment.
+----------------------------------------------------------------------------------------
+*/
+
+includeConfig 'affy.config'
+
+params {
+    paramset_name     = 'affy_limma_gprofiler2'
+    functional_method = 'gprofiler2'
+}

conf/affy/affy_limma_gsea.config

@@ -0,0 +1,14 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Affymetrix Limma + GSEA analysis profile
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Inherits from affy.config and adds GSEA functional enrichment.
+----------------------------------------------------------------------------------------
+*/
+
+includeConfig 'affy.config'
+
+params {
+    paramset_name     = 'affy_limma_gsea'
+    functional_method = 'gsea'
+}

conf/maxquant/maxquant.config

@@ -0,0 +1,45 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    MaxQuant proteomics analysis profile (default: Limma)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Sets parameters for MaxQuant proteomics differential abundance analysis using Limma.
+    Use as follows:
+        nextflow run nf-core/differentialabundance -profile maxquant,<docker/singularity> --input <SAMPLESHEET> --matrix <MATRIX> --outdir <OUTDIR>
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    paramset_name                    = 'maxquant'
+
+    // Study
+    study_type                       = 'maxquant'
+    study_abundance_type             = 'intensities'
+
+    // Differential analysis (Limma)
+    differential_method              = 'limma'
+
+    // Features
+    features_id_col                  = 'Majority protein IDs'
+    features_name_col                = 'Majority protein IDs'
+    features_metadata_cols           = 'Majority protein IDs'
+    features_type                    = 'protein'
+    differential_feature_id_column   = 'Majority protein IDs'
+    differential_feature_name_column = 'Majority protein IDs'
+
+    // Exploratory
+    exploratory_assay_names          = 'raw,normalised'
+    exploratory_final_assay          = 'normalised'
+    exploratory_log2_assays          = null
+
+    // Differential output columns
+    differential_file_suffix         = '.limma.results.tsv'
+    differential_fc_column           = 'logFC'
+    differential_pval_column         = 'P.Value'
+    differential_qval_column         = 'adj.P.Val'
+
+    // Proteus
+    proteus_measurecol_prefix        = 'LFQ intensity'
+
+    // Shiny app
+    shinyngs_build_app               = false
+}