From adbc14f7caef3e0c3c83657ba2d3d88f33a5380f Mon Sep 17 00:00:00 2001 From: WackerO Date: Tue, 19 Mar 2024 15:08:05 +0100 Subject: [PATCH 01/12] Added QBiC credits, made observations_name_col optional on modules.config, changed features_id/name_col helptext --- README.md | 2 +- conf/modules.config | 8 +++----- conf/test.config | 1 - nextflow_schema.json | 6 +++--- 4 files changed, 7 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 889f577c..66e46c8d 100644 --- a/README.md +++ b/README.md @@ -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. 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: diff --git a/conf/modules.config b/conf/modules.config index 5e4a36de..a2d0f2e1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -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 \"${params.observations_name_col}\""), "--file_name_col \"${params.affy_file_name_col}\"", "--background ${params.affy_background}", "--normalize False", "--bgversion ${params.affy_bgversion}", - "--file_name_col \"${params.affy_file_name_col}\"", "--destructive ${params.affy_destructive}", "--rm.mask ${params.affy_rm_mask}", "--rm.outliers ${params.affy_rm_outliers}", @@ -86,12 +85,11 @@ process { ] ext.prefix = { "normalised." } ext.args = { [ - "--sample_name_col \"${params.observations_name_col}\"", + ((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""), "--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 ${params.affy_rm_outliers}", @@ -423,7 +421,7 @@ process { "--assay_names \"${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 \"${params.features_name_col}\""), "--diff_feature_id_col \"${params.differential_feature_id_column}\"", "--fold_change_column \"${params.differential_fc_column}\"", "--pval_column \"${params.differential_pval_column}\"", diff --git a/conf/test.config b/conf/test.config index 4d4e9454..49cce2f7 100644 --- a/conf/test.config +++ b/conf/test.config @@ -34,7 +34,6 @@ params { // Observations observations_id_col = 'sample' - observations_name_col = 'sample' // Apply a higher filter to check that the filtering works filtering_min_abundance=10 diff --git a/nextflow_schema.json b/nextflow_schema.json index acb712b5..7a688e8c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -119,7 +119,6 @@ }, "observations_name_col": { "type": "string", - "default": "sample", "description": "Column in the sample sheet to be used as the display identifier for observations", "fa_icon": "fas fa-file-signature" } @@ -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": { @@ -1014,6 +1013,7 @@ "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$", "fa_icon": "fas fa-book" From 65550c5a95667a5533a84ceed3440880e28564b3 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Mar 2024 13:37:01 +0100 Subject: [PATCH 02/12] Moved differential_file_suffix and exploratory_assay_names to advanced options, made suffix an optional param2 --- assets/differentialabundance_report.Rmd | 7 +++-- nextflow.config | 7 +++-- nextflow_schema.json | 37 +++++++++++++++---------- 3 files changed, 32 insertions(+), 19 deletions(-) diff --git a/assets/differentialabundance_report.Rmd b/assets/differentialabundance_report.Rmd index 1c509001..26fb7f4e 100644 --- a/assets/differentialabundance_report.Rmd +++ b/assets/differentialabundance_report.Rmd @@ -360,9 +360,12 @@ treatment-mCherry-hND6-batcheffect.deseq2.results.tsv --> ```{r, echo=FALSE} - +differential_file_suffix <- params$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){ diff --git a/nextflow.config b/nextflow.config index 055bfa4e..95076f4f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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" @@ -188,6 +186,11 @@ params { // Gene set options gene_sets_files = null + // Advanced options + differential_file_suffix = null + exploratory_assay_names = "raw,normalised,variance_stabilised" + + // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' diff --git a/nextflow_schema.json b/nextflow_schema.json index 7a688e8c..b24b171a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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", @@ -388,13 +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", @@ -425,12 +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", @@ -499,7 +486,6 @@ } }, "required": [ - "differential_file_suffix", "differential_feature_id_column", "differential_fc_column", "differential_qval_column", @@ -1080,6 +1066,27 @@ }, "required": ["report_file", "logo_file", "css_file"] }, + "advanced_options": { + "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", From 5c08b3bb1100039af3bd3347a1fba30adc8454d0 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Mar 2024 15:21:18 +0100 Subject: [PATCH 03/12] linting --- nextflow_schema.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index b24b171a..b485115e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1333,6 +1333,9 @@ { "$ref": "#/definitions/reporting_options" }, + { + "$ref": "#/definitions/advanced_options" + }, { "$ref": "#/definitions/reference_genome_options" }, From 13899f432de08408c5a0999c2a8fded2eefe71a0 Mon Sep 17 00:00:00 2001 From: WackerO Date: Wed, 20 Mar 2024 15:23:38 +0100 Subject: [PATCH 04/12] updated changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cb15bcd3..9e7351ab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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)) @@ -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)) From 37fa90a978953acdf122b917b5065d98f25372dc Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Thu, 21 Mar 2024 12:29:09 +0100 Subject: [PATCH 05/12] Update README.md Co-authored-by: Jonathan Manning --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 66e46c8d..adaee862 100644 --- a/README.md +++ b/README.md @@ -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. 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. +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 the support of open science in this project. 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: From a64c11a684ff30edda58fb52c4f82f84114d69df Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Thu, 21 Mar 2024 12:29:56 +0100 Subject: [PATCH 06/12] Update conf/modules.config Co-authored-by: Jonathan Manning --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index a2d0f2e1..167ef943 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -62,7 +62,7 @@ process { ] ext.prefix = { "raw." } ext.args = { [ - ((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""), + "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"", "--file_name_col \"${params.affy_file_name_col}\"", "--background ${params.affy_background}", "--normalize False", From 0c352ebe682f23252600bc4aa2f6e6b9ba183267 Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Thu, 21 Mar 2024 12:30:21 +0100 Subject: [PATCH 07/12] Update conf/modules.config Co-authored-by: Jonathan Manning --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 167ef943..04e011f1 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -85,7 +85,7 @@ process { ] ext.prefix = { "normalised." } ext.args = { [ - ((params.observations_name_col == null) ? "--sample_name_col \"${params.observations_id_col}\"" : "--sample_name_col \"${params.observations_name_col}\""), + "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"", "--file_name_col \"${params.affy_file_name_col}\"", "--background ${params.affy_background}", "--normalize True", From ba94655b7c9baf1bb58a739418a3eb8b33094525 Mon Sep 17 00:00:00 2001 From: WackerO <43847497+WackerO@users.noreply.github.com> Date: Thu, 21 Mar 2024 12:30:30 +0100 Subject: [PATCH 08/12] Update conf/modules.config Co-authored-by: Jonathan Manning --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 04e011f1..3dd4a35a 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -421,7 +421,7 @@ process { "--assay_names \"${params.exploratory_assay_names}\"", "--sample_id_col \"${params.observations_id_col}\"", "--feature_id_col \"${params.features_id_col}\"", - ((params.features_name_col == null) ? "--feature_name_col \"${params.features_id_col}\"" : "--feature_name_col \"${params.features_name_col}\""), + "--feature_name_col \"" + (params.features_name_col == null ? params.features_id_col : params.features_name_col) + "\"", "--diff_feature_id_col \"${params.differential_feature_id_column}\"", "--fold_change_column \"${params.differential_fc_column}\"", "--pval_column \"${params.differential_pval_column}\"", From 1f1566607c3d348001133b394af28d12858bec8e Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 21 Mar 2024 14:35:52 +0100 Subject: [PATCH 09/12] Returned advanced options to their sections, removed default for observations_name_col --- nextflow.config | 9 +++------ nextflow_schema.json | 33 ++++++++++++--------------------- 2 files changed, 15 insertions(+), 27 deletions(-) diff --git a/nextflow.config b/nextflow.config index 95076f4f..c7130eae 100644 --- a/nextflow.config +++ b/nextflow.config @@ -36,7 +36,7 @@ params { // Sample sheet options observations_type = 'sample' observations_id_col = 'sample' - observations_name_col = 'sample' + observations_name_col = null // Feature options features = null @@ -84,10 +84,12 @@ 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 = null differential_feature_id_column = "gene_id" differential_feature_name_column = "gene_name" differential_fc_column = "log2FoldChange" @@ -186,11 +188,6 @@ params { // Gene set options gene_sets_files = null - // Advanced options - differential_file_suffix = null - exploratory_assay_names = "raw,normalised,variance_stabilised" - - // References genome = null igenomes_base = 's3://ngi-igenomes/igenomes/' diff --git a/nextflow_schema.json b/nextflow_schema.json index b485115e..116f1396 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -388,6 +388,13 @@ "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", @@ -418,6 +425,11 @@ "description": "Options related to differential operations", "default": "", "properties": { + "differential_file_suffix": { + "type": "string", + "description": "Advanced option: the suffix associated tabular differential results tables. Will by default use the appropriate suffix according to the study_type.", + "fa_icon": "fas fa-signature" + }, "differential_feature_id_column": { "type": "string", "default": "gene_id", @@ -1066,27 +1078,6 @@ }, "required": ["report_file", "logo_file", "css_file"] }, - "advanced_options": { - "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", From 8fa83dd0b975d9c40cec595c6aaa8aaa020171ca Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 21 Mar 2024 14:36:23 +0100 Subject: [PATCH 10/12] linting --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 3dd4a35a..5fbb5421 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -62,7 +62,7 @@ process { ] ext.prefix = { "raw." } ext.args = { [ - "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"", + "--sample_name_col \"" + (params.observations_name_col == null ? params.observations_id_col : params.observations_name_col) + "\"", "--file_name_col \"${params.affy_file_name_col}\"", "--background ${params.affy_background}", "--normalize False", From 82cba18c56261a2b9b6ed784326e7760e742894b Mon Sep 17 00:00:00 2001 From: WackerO Date: Thu, 21 Mar 2024 14:43:17 +0100 Subject: [PATCH 11/12] removed advanced options key from schema, re-added example of observations_name_col --- conf/test.config | 1 + nextflow_schema.json | 3 --- 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index 49cce2f7..4d4e9454 100644 --- a/conf/test.config +++ b/conf/test.config @@ -34,6 +34,7 @@ params { // Observations observations_id_col = 'sample' + observations_name_col = 'sample' // Apply a higher filter to check that the filtering works filtering_min_abundance=10 diff --git a/nextflow_schema.json b/nextflow_schema.json index 116f1396..f9603f80 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1324,9 +1324,6 @@ { "$ref": "#/definitions/reporting_options" }, - { - "$ref": "#/definitions/advanced_options" - }, { "$ref": "#/definitions/reference_genome_options" }, From 0854d3f53526d9fb1e2dce9c17288f85c65eb6eb Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 22 Mar 2024 14:28:48 +0100 Subject: [PATCH 12/12] added description of observations_name_col default --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index f9603f80..f9826d19 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -119,7 +119,7 @@ }, "observations_name_col": { "type": "string", - "description": "Column in the sample sheet to be used as the display identifier for observations", + "description": "Column in the sample sheet to be used as the display identifier for observations. If unset, will use value of --observations_id_col.", "fa_icon": "fas fa-file-signature" } },