add sample_name as possible column in samplesheet
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kylacochrane
approved these changes
Oct 25, 2024
apetkau
approved these changes
Oct 28, 2024
emarinier
requested changes
Oct 29, 2024
CHANGELOG.md
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| - Added the ability to include a `sample_name` column in the input samplesheet.csv. Allows for compatibility with IRIDA-Next input configuration. | ||
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| - `sample_name` special characters will be replaced with `"_"` |
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Might be useful to include what characters are special (non-alphanumeric?).
README.md
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| `sample_name`: An **optional** column, that overrides `sample` for outputs (filenames and sample names) and reference assembly identification. | ||
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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 the comma after sample_name might be unneeded.
workflows/gasclustering.nf
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| ID_COLUMN = "sample_name" | ||
| ID_COLUMN2 = "sample" |
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I would recommend changing ID_COLUMN and ID_COLUMN2 to something more like SAMPLE_NAME_COLUMN and SAMPLE_COLUMN, or ID_SAMPLE_NAME and ID_SAMPLE, so that's it's more clear the difference between the two when reading the code.
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Also, is ID_COLUMN used within the code? If it's not, it should probably be removed and maybe that changes the name to ID_HEADER or something?
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Good catch ID_COLUMN is a vestige from some testing. Well, really I should remove ID_COLUMN2, and replace with ID_COLUMN = "sample".
It goes into the formatting of the metadata_headers channel:
metadata_headers = Channel.of(
tuple(
ID_COLUMN2,
params.metadata_1_header, params.metadata_2_header,
params.metadata_3_header, params.metadata_4_header,
params.metadata_5_header, params.metadata_6_header,
params.metadata_7_header, params.metadata_8_header)
)
I think I will change it to SAMPLE_HEADER so it fits nicely in the channel. Here d877ee2
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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 for example. What this means is that the output files and thesamplename will be changed tosample_nameif asample_nameis called. Ifgasclusteringis 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>).nf-testto test new featuredocs/usage.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).