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Some parameter changes, added qbic credits #254

Merged
merged 12 commits into from
Mar 22, 2024
4 changes: 3 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Added advanced params section, added QBiC credits ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#250](https://github.com/nf-core/differentialabundance/pull/250)] - Template update for nf-core/tools v2.13.1 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#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))
Expand All @@ -17,7 +18,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [[#240](https://github.com/nf-core/differentialabundance/pull/240) - Publish GSEA reports ([@pinin4fjords](https://github.com/pinin4fjords), review by )
- [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Made differential_file_suffix optional ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#240](https://github.com/nf-core/differentialabundance/pull/240)] - Publish GSEA reports ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#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))
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -110,7 +110,7 @@ For more details about the output files and reports, please refer to the

## Credits

nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. We are grateful for their support of open science in this project.
nf-core/differentialabundance was originally written by Jonathan Manning ([@pinin4fjords](https://github.com/pinin4fjords)) and Oskar Wacker ([@WackerO](https://github.com/WackerO)). Jonathan Manning (now at Seqera) initially worked on this workflow as an employee of Healx, an AI-powered, patient-inspired tech company, accelerating the discovery and development of treatments for rare diseases. Oskar Wacker works for [QBiC](https://www.qbic.uni-tuebingen.de/) at Tübingen University. We are grateful for their support of open science in this project.
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We thank the many members of the nf-core community who assisted with this pipeline, often by reviewing module pull requests including but not limited to:

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7 changes: 5 additions & 2 deletions assets/differentialabundance_report.Rmd
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Expand Up @@ -360,9 +360,12 @@ treatment-mCherry-hND6-batcheffect.deseq2.results.tsv
-->

```{r, echo=FALSE}

differential_file_suffix <- params$differential_file_suffix
if (is.null(differential_file_suffix)) {
differential_file_suffix <- ifelse(params$study_type %in% c('rnaseq'), ".deseq2.results.tsv", ".limma.results.tsv")
}
differential_files <- lapply(contrasts$id, function(d){
file.path(params$input_dir, paste0(gsub(' |;', '_', d), params$differential_file_suffix))
file.path(params$input_dir, paste0(gsub(' |;', '_', d), differential_file_suffix))
})

differential_results <- lapply(differential_files, function(diff_file){
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8 changes: 3 additions & 5 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -62,12 +62,11 @@ process {
]
ext.prefix = { "raw." }
ext.args = { [
"--sample_name_col \"${params.observations_name_col}\"",
((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""),
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"--file_name_col \"${params.affy_file_name_col}\"",
"--background ${params.affy_background}",
"--normalize False",
"--bgversion ${params.affy_bgversion}",
"--file_name_col \"${params.affy_file_name_col}\"",
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"--destructive ${params.affy_destructive}",
"--rm.mask ${params.affy_rm_mask}",
"--rm.outliers ${params.affy_rm_outliers}",
Expand All @@ -86,12 +85,11 @@ process {
]
ext.prefix = { "normalised." }
ext.args = { [
"--sample_name_col \"${params.observations_name_col}\"",
((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""),
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"--file_name_col \"${params.affy_file_name_col}\"",
"--background ${params.affy_background}",
"--normalize True",
"--bgversion ${params.affy_bgversion}",
"--file_name_col \"${params.affy_file_name_col}\"",
"--destructive ${params.affy_destructive}",
"--rm.mask ${params.affy_rm_mask}",
"--rm.outliers ${params.affy_rm_outliers}",
Expand Down Expand Up @@ -423,7 +421,7 @@ process {
"--assay_names \"${params.exploratory_assay_names}\"",
"--sample_id_col \"${params.observations_id_col}\"",
"--feature_id_col \"${params.features_id_col}\"",
"--feature_name_col \"${params.features_name_col}\"",
((params.features_name_col == null) ? "--feature_name_col \"${params.features_id_col}\"" : "--feature_name_col \"${params.features_name_col}\""),
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"--diff_feature_id_col \"${params.differential_feature_id_column}\"",
"--fold_change_column \"${params.differential_fc_column}\"",
"--pval_column \"${params.differential_pval_column}\"",
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1 change: 0 additions & 1 deletion conf/test.config
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ params {

// Observations
observations_id_col = 'sample'
observations_name_col = 'sample'
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// Apply a higher filter to check that the filtering works
filtering_min_abundance=10
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7 changes: 5 additions & 2 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -84,12 +84,10 @@ params {
exploratory_n_features = 500
exploratory_whisker_distance = 1.5
exploratory_mad_threshold = -5
exploratory_assay_names = "raw,normalised,variance_stabilised"
exploratory_final_assay = "variance_stabilised"
exploratory_palette_name = 'Set1'

// Differential options
differential_file_suffix = ".deseq2.results.tsv"
differential_feature_id_column = "gene_id"
differential_feature_name_column = "gene_name"
differential_fc_column = "log2FoldChange"
Expand Down Expand Up @@ -188,6 +186,11 @@ params {
// Gene set options
gene_sets_files = null

// Advanced options
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differential_file_suffix = null
exploratory_assay_names = "raw,normalised,variance_stabilised"


// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
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46 changes: 28 additions & 18 deletions nextflow_schema.json
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Expand Up @@ -80,7 +80,7 @@
"type": "string",
"fa_icon": "fas fa-border-all",
"description": "(RNA-seq only): optional transcript length matrix with samples and genes as the abundance matrix",
"help_text": "if provided, this file willl be used to provide transcript lengths to DESeq2 to model length bias across samples"
"help_text": "If provided, this file willl be used to provide transcript lengths to DESeq2 to model length bias across samples"
},
"affy_cel_files_archive": {
"type": "string",
Expand Down Expand Up @@ -119,7 +119,6 @@
},
"observations_name_col": {
"type": "string",
"default": "sample",
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Maybe mention in the description that we will now default to the same column as the ID?

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done!

"description": "Column in the sample sheet to be used as the display identifier for observations",
"fa_icon": "fas fa-file-signature"
}
Expand All @@ -137,13 +136,13 @@
"features_id_col": {
"type": "string",
"default": "gene_id",
"description": "Feature ID attribute in the GTF file (e.g. the gene_id field)",
"description": "Feature ID attribute in the abundance table as well as in the GTF file (e.g. the gene_id field)",
"fa_icon": "fas fa-address-card"
},
"features_name_col": {
"type": "string",
"default": "gene_name",
"description": "Feature name attribute in the GTF file (e.g. the gene symbol field)",
"description": "Feature name attribute in the abundance table as well as in the GTF file (e.g. the gene symbol field)",
"fa_icon": "fas fa-signature"
},
"features_type": {
Expand Down Expand Up @@ -389,13 +388,6 @@
"help_text": "Some plots are only generated once, with a single sample grouping, this option defines how that sample grouping is selected. It should be 'auto_pca' (variable selected from the sample sheet with the most association with the first principal component), 'contrasts' (pick the variable associated with the first contrast), or a value specifying a specific column in the observations.",
"fa_icon": "fas fa-home"
},
"exploratory_assay_names": {
"type": "string",
"default": "raw,normalised,variance_stabilised",
"hidden": true,
"description": "Specifies assay names to be used for matrices, platform-specific",
"fa_icon": "fas fa-file-signature"
},
"exploratory_final_assay": {
"type": "string",
"default": "variance_stabilised",
Expand Down Expand Up @@ -426,12 +418,6 @@
"description": "Options related to differential operations",
"default": "",
"properties": {
"differential_file_suffix": {
"type": "string",
"default": ".deseq2.results.tsv",
"description": "The suffix associated tabular differential results tables",
"fa_icon": "fas fa-signature"
},
"differential_feature_id_column": {
"type": "string",
"default": "gene_id",
Expand Down Expand Up @@ -500,7 +486,6 @@
}
},
"required": [
"differential_file_suffix",
"differential_feature_id_column",
"differential_fc_column",
"differential_qval_column",
Expand Down Expand Up @@ -1014,6 +999,7 @@
"report_file": {
"type": "string",
"description": "Rmd report template from which to create the pipeline report",
"help_text": "The pipeline will always generate a default report which gives a good overview of the analysis results. Should this default report not suit your needs, you can provide the path to a custom report instead.",
"format": "file-path",
"pattern": "^\\S+\\.Rmd$",
"fa_icon": "fas fa-book"
Expand Down Expand Up @@ -1080,6 +1066,27 @@
},
"required": ["report_file", "logo_file", "css_file"]
},
"advanced_options": {
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"title": "Advanced options",
"type": "object",
"description": "",
"default": "",
"properties": {
"differential_file_suffix": {
"type": "string",
"description": "The suffix associated tabular differential results tables",
"fa_icon": "fas fa-signature"
},
"exploratory_assay_names": {
"type": "string",
"default": "raw,normalised,variance_stabilised",
"hidden": true,
"description": "Specifies assay names to be used for matrices, platform-specific",
"fa_icon": "fas fa-file-signature"
}
},
"required": ["differential_file_suffix", "exploratory_assay_names"]
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
Expand Down Expand Up @@ -1326,6 +1333,9 @@
{
"$ref": "#/definitions/reporting_options"
},
{
"$ref": "#/definitions/advanced_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
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