diff --git a/modules/nf-core/shinyngs/app/meta.yml b/modules/nf-core/shinyngs/app/meta.yml index a695351de6a..1c5cb8311ba 100644 --- a/modules/nf-core/shinyngs/app/meta.yml +++ b/modules/nf-core/shinyngs/app/meta.yml @@ -34,7 +34,7 @@ input: description: | TSV-format feature (e.g. gene) metadata - assay_files: - type: list + type: file description: | List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - contrasts: @@ -42,7 +42,7 @@ input: description: | CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. - differential_results: - type: list + type: file description: | List of TSV-format differential analysis outputs, one per row of the contrasts file diff --git a/modules/nf-core/shinyngs/staticdifferential/meta.yml b/modules/nf-core/shinyngs/staticdifferential/meta.yml index 22ec8a77b0a..84fe31de385 100644 --- a/modules/nf-core/shinyngs/staticdifferential/meta.yml +++ b/modules/nf-core/shinyngs/staticdifferential/meta.yml @@ -27,7 +27,7 @@ input: features and samples, at a minimum an id. e.g. [ id:'test' ] - differential_results: - type: list + type: file description: | CSV or TSV-format tabular file with differential analysis outputs - sample: @@ -39,7 +39,7 @@ input: description: | CSV or TSV-format feature (e.g. gene) metadata - assay_file: - type: list + type: file description: | CSV or TSV matrix file to use alongside differential statistics in interpretation. Usually a normalised form. @@ -50,11 +50,16 @@ output: description: | Groovy Map containing contrast information e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - volcanos: - type: tuple + - volcanos_png: + type: file + description: | + Meta-keyed tuple containing a PNG output for a volcano plot built from + the differential result table. + - volcanos_html: + type: file description: | - Meta-keyed tuple containing a PNG and HTML plot for a volcano plot - built from the differential result table. + Meta-keyed tuple containing an HTML output for a volcano plot built + from the differential result table. - versions: type: file description: File containing software versions diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf index 9b40a3380ae..4c33b3cba1c 100644 --- a/modules/nf-core/shinyngs/staticexploratory/main.nf +++ b/modules/nf-core/shinyngs/staticexploratory/main.nf @@ -19,7 +19,7 @@ process SHINYNGS_STATICEXPLORATORY { tuple val(meta), path("*/html/pca2d.html") , emit: pca2d_html, optional: true tuple val(meta), path("*/png/pca3d.png") , emit: pca3d_png tuple val(meta), path("*/html/pca3d.html") , emit: pca3d_html, optional: true - tuple val(meta), path("*/png/mad_correlation.png") , emit: mad_png + tuple val(meta), path("*/png/mad_correlation.png") , emit: mad_png, optional: true tuple val(meta), path("*/html/mad_correlation.html") , emit: mad_html, optional: true tuple val(meta), path("*/png/sample_dendrogram.png") , emit: dendro path "versions.yml" , emit: versions diff --git a/modules/nf-core/shinyngs/staticexploratory/meta.yml b/modules/nf-core/shinyngs/staticexploratory/meta.yml index 008214f90a6..6f745da5cef 100644 --- a/modules/nf-core/shinyngs/staticexploratory/meta.yml +++ b/modules/nf-core/shinyngs/staticexploratory/meta.yml @@ -30,40 +30,64 @@ input: description: | TSV-format feature (e.g. gene) metadata - assay_files: - type: list + type: file description: | List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). output: - - boxplots: - type: tuple + - boxplots_png: + type: file + description: | + Meta-keyed tuple containing PNG output for box plots covering input + matrices. + - boxplots_html: + type: file + description: | + Meta-keyed tuple containing HTML output for box plots covering input + matrices. + - densities_png: + type: file description: | - Meta-keyed tuple containing a PNG and HTML output for box plots + Meta-keyed tuple containing PNG output for density plots covering input matrices. - - densities: - type: tuple + - densities_html: + type: file description: | - Meta-keyed tuple containing a PNG and HTML output for density plots + Meta-keyed tuple containing HTML output for density plots covering input matrices. - - pca2d: - type: tuple + - pca2d_png: + type: file + description: | + Meta-keyed tuple containing a PNG output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - pca2d_html: + type: file description: | - Meta-keyed tuple containing a PNG and HTML plot for 2D PCA plots + Meta-keyed tuple containing an HTML output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - pca3d_png: + type: file + description: | + Meta-keyed tuple containing a PNG output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - pca3d_html: + type: file + description: | + Meta-keyed tuple containing an HTML output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - mad_png: + type: file + description: | + Meta-keyed tuple containing a PNG output for MAD correlation plots covering specified input matrix (by default the last one in the input list. - - pca3d: - type: tuple + - mad_dendro: + type: file description: | - Meta-keyed tuple containing a PNG and HTML plot for 3D PCA plots + Meta-keyed tuple containing an HTML output for MAD correlation plots covering specified input matrix (by default the last one in the input list. - - mad: - type: tuple - description: | - Meta-keyed tuple containing a PNG and HTML plot for MAD correlation - plots covering specified input matrix (by default the last one in the - input list. - dendro: - type: tuple + type: file description: | Meta-keyed tuple containing a PNG, for a sample clustering dendrogramcovering specified input matrix (by default the last one in diff --git a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml index 0cf380da2f9..7ad75968ff0 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml @@ -3,6 +3,9 @@ description: validate consistency of feature and sample annotations with matrice keywords: - expression + - features + - observations + - validation tools: - "shinyngs": @@ -42,7 +45,7 @@ input: description: | TSV-format feature (e.g. gene) metadata - assay_files: - type: list + type: file description: | List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - contrasts: