[PROOF OF PRINCIPLE] Rename publish_by_id to publish_by_meta and add flexibility of taking a list of ids #590
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grst
reviewed
Apr 8, 2021
drpatelh
commented
Apr 8, 2021
drpatelh
changed the title
wkang0
approved these changes
Apr 8, 2021
| path = path instanceof String ? path : id | ||
| path_list.add(path) | ||
| } | ||
| } | ||
| } |
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What happens when the id is not String for example: publish_by_meta = [1, 2, 3] or when the meta[id] is true/false?
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If the key is not a String it will be ignored via the statement below:
if (args.meta && key instanceof String) {
| for (id in publish_id_list) { | ||
| if (args.meta && id instanceof String) { | ||
| def path = args.meta.containsKey(id) ? args.meta[id] : id | ||
| path = path instanceof String ? path : id |
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Looks like all non-String path would be ignored. Would you try to convert the path to String here? Is it possible to treat boolean value to be yes/no and append it to the end of the key? Also, can you replace id to key in the for loop so that it won't be confused between meta['id'] and meta[id]?
wkang0
suggested changes
Apr 8, 2021
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Please don't forget to update the modules.conf header part:
/*
-
- Config file for defining DSL2 per module options
-
- Available keys to override module options:
-
args = Additional arguments appended to command in module. -
args2 = Second set of arguments appended to command in module (multi-tool modules). -
publish_dir = Directory to publish results. -
publish_by_meta = Groovy list of keys available in meta map to append as directories to "publish_dir" path -
If publish_by_meta = true - Value of ${meta['id']} is appended as a directory to "publish_dir" path -
If publish_by_meta = ['id', 'custompath'] - If "id" is in meta map and "custompath" isn't then "${meta['id']}/custompath/" -
is appended as a directory to "publish_dir" path -
If publish_by_meta = false / null - No directories are appended to "publish_dir" path -
publish_files = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension -
The value of "directory" is appended to the standard "publish_dir" path as defined above. -
If publish_files = null (unspecified) - All files are published. -
If publish_files = false - No files are published. -
suffix = File name suffix for output files.
*/
This was referenced Apr 9, 2021
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Added in nf-core/modules#423 and #591 |
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PR checklist
nf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).