Repository navigation
Conversation
| "type": "string" | ||
| }, | ||
| "ref_ncbi_query_max": { | ||
| "type": "string", |
|
| }, | ||
| "template": { | ||
| "type": "string", | ||
| "default": "report", |
Comment on lines
+1209
to
+1211
| if (grepl('^~', value)) { | ||
| stop(call. = FALSE, paste0('report_data template "', value, '" starts with "~", which is not expanded.')) | ||
| } |
| stop(call. = FALSE, paste0('report_data template "', value, '" starts with "~", which is not expanded.')) | ||
| } | ||
| candidates <- value | ||
| if (!grepl('^/', value)) { |
There was a problem hiding this comment.
test if matches a dir name in assets/report_templates, if it exists use it even if a relative path also matches
| # Replace double quotes with single quotes to not conflict with the CSV format quoting values | ||
| metadata_samp[] <- lapply(metadata_samp, gsub, pattern = '"', replacement = "'") | ||
| metadata_ref[] <- lapply(metadata_ref, gsub, pattern = '"', replacement = "'") | ||
| metadata_rep[] <- lapply(metadata_rep, gsub, pattern = '"', replacement = "'") |
|
|
||
| This is the primary output of the pipeline, containing the report meant to be understandable by non-bioinformaticians. | ||
|
|
||
| Each full report directory contains the rendered site, so every page of a multi-page template is included along with the stylesheets, scripts and images those pages reference. A `render_target` publishes only the exact matching rendered file. |
There was a problem hiding this comment.
generalize to any quarto template output or just talk about defualt repor
| export XDG_CACHE_HOME="\$(pwd)/cache" | ||
|
|
||
| # Render a private copy; the staged template may be a symlink to user data. | ||
| cp -r --dereference render_report_template render_report |
Comment on lines
+60
to
+66
| shopt -s nullglob dotglob | ||
| rendered_entries=( "\$site_dir"/* ) | ||
| shopt -u nullglob dotglob | ||
| if [[ -d "\$site_dir" && \${#rendered_entries[@]} -gt 0 ]]; then | ||
| mkdir -p "${prefix}" | ||
| cp -R "\$site_dir/." "${prefix}/" | ||
| fi |
There was a problem hiding this comment.
check if can be replaced with cp --dereference
Comment on lines
+295
to
+298
| .map { row -> | ||
| def report_meta = [id: row.report_group_ids.toString()] | ||
| def template_meta = [template: row.template.toString(), render_target: row.render_target.toString()] | ||
| [report_meta, template_meta, file(row.template.toString(), checkIfExists: true)] |
There was a problem hiding this comment.
move parsing logic to PREPARE_INPUT and use same methods that are used to parse sample and reference metadata so that we dont need to hardcode column names
Comment on lines
+1213
to
+1217
| expanded_value <- path.expand(value) | ||
| candidates <- expanded_value | ||
| if (!grepl('^/', expanded_value)) { | ||
| candidates <- c(candidates, file.path(projectDir, expanded_value)) | ||
| } |
There was a problem hiding this comment.
too complex, if it exists use it, otherwise error
| | ------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | `report_group_ids` | Report group IDs defined in the sample metadata. Can accept multiple values if delimited by semicolons. | | ||
| | `template` | A pre-built template directory name under `assets/report_templates/` (for example, `pathsurveil_report`) or a path to a custom template directory. Existing paths are checked before pre-built names. Multiple templates may be delimited by semicolons. | | ||
| | `template` | A pre-built template directory name under `assets/report_templates/` (for example, `pathsurveil_report`) or a path to a custom template directory. Built-in template names are checked first; otherwise relative, `~`-prefixed, and absolute paths are supported. Multiple templates may be delimited by semicolons. | |
There was a problem hiding this comment.
dont need dewtail on different types of paths
| def template_meta = [ | ||
| template: row.template.toString(), | ||
| render_target: row.render_target.toString() | ||
| ] |
There was a problem hiding this comment.
like ref_meta = ref_meta.collectEntries { key, value -> [(key): value ?: null] }
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).