Update: Include sample_name IRIDA-Next input column #26
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Tested it in IRIDA-Next locally. Looks good! |
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An issue that has arisen due to these changes is that when we modify the |
emarinier
requested changes
Sep 18, 2024
kylacochrane
previously approved these changes
Sep 18, 2024
kylacochrane
requested changes
Sep 19, 2024
CHANGELOG.md
Outdated
| - Modified the template for input csv file to include a `sample_name` column in addition to `sample` in-line with changes to [IRIDA-Next update] as seen with the [speciesabundance pipeline] | ||
| - `sample_name` special characters will be replaced with `"_"` | ||
| - If no `sample_name` is supplied in the column `sample` will be used | ||
| - To avoid repeat values for `sample_name` all `sample_name` values will be suffixed with the index of the `input` samplesheet.csv |
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Just checking on this - is the plan to use the index or append sample_name?
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There is always one place in documentation where I forget to update things to the newest version! Thanks for catching this!
| `sample` is a unique identifier, designed to be used internally or in IRIDA-Next, or when `sample_name` is not provided. | ||
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| `sample_name`, allows more flexibility in naming output files or sample identification. Unlike `sample`, `sample_name` is not required to contain unique values. `Nextflow` requires unique sample names, and therefore in the instance of repeat `sample_names`, `sample` will be suffixed to any `sample_name`. Non-alphanumeric characters (excluding `_`,`-`,`.`) will be replaced with `"_"`. | ||
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I think this description was much needed!!!
Just one comment on how it slightly differs from the CHANGELOG.md where index was suggested as the suffix should there be repeat sample_names 😄
| @@ -243,7 +261,8 @@ def select_reference(refgenome, reference_sample_id, sample_assemblies) { | |||
| log.debug "Selecting reference genome ${reference_genome} from '--refgenome'." | |||
| } | |||
| else if (reference_sample_id) { | |||
| reference_genome = sample_assemblies.filter { it[0] == reference_sample_id && it[1] != null} | |||
| // Check each meta category (meta.id, meta.id_alt, meta.irida_id) for a match to params.reference_sample_id | |||
| reference_genome = sample_assemblies.filter { (it[0].id == reference_sample_id || it[0].irida_id == reference_sample_id || it[0].id_alt == reference_sample_id) && it[1] != null} | |||
| .ifEmpty { error("The provided reference sample ID (${reference_sample_id}) is either missing or has no associated reference assembly.") } | |||
apetkau
approved these changes
Sep 23, 2024
kylacochrane
approved these changes
Sep 23, 2024
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Added in a change suggested by @emarinier to remove the necessity of adding in meta.id_alt to the schema. |
emarinier
approved these changes
Sep 23, 2024
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Rather than troubleshooting why the change without |
Merged
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Modified the template for input
samplesheet.csvfile to include thesample_namecolumn in addition tosamplein-line with changes to IRIDA-Next update as seen with the speciesabundance pipeline and staramrnf. What this means is that the output files and thesamplename will be changed tosample_nameif asample_nameis called. Ifsnvphylnfcis being locally then thesample_namecan be left blank.Made a few changes:
-
sample_namespecial characters will be replaced with"_"- If no
sample_nameis supplied in the columnsamplewill be used- To avoid repeat values for
sample_nameallsample_namevalues will be suffixed withsample- Tests to check that the variety of different
sample_nameswork with thePR checklist
nf-core lint).nextflow run . -profile 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).