Add package: 2025_Maravall_Lopez_Argentina - #204
Conversation
|
@delphis-bot create recipe |
|
SSF files MUST be named after their respective package. The following SSF files break this rule: |
|
@delphis-bot create recipe |
|
@TCLamnidis I have uploaded both the .janno and SSF file. In the .janno file in the columns UDG and Library_Built for the samples that had multiple libraries I kept the least udg treated (for example if there were both half and plus libraries, I wrote down half) and ds if there was a mix of ds and ss, even though in the publication they provide info for each library separately. If needed I can reupload with the info for each library separated by ;. In the Endogenous column a different number was provided for each library in the publication and I left that as it was, each number separated by ;. That created an issue in the .janno validation. Let me know if I should fix that. |
Linked to #198
PR Checklist
Add/Update package: {package_name}.update. (Add to
Linked to #198above.)If adding or updating a package:
SSF file Todo list
.ssf) for the requestedpackage.
.ssffile(s) matches the package name (i.e.packages/2023_my_package/2023_my_package.ssf)..ssffile MUST contain a new line at the end of the file.A check for this exists in the CI. This check should pass before
you continue with this list.
poseidon_IDs,udg, andlibrary_builtare filledand correct.
noteswhere necessary to explain any specialcases/judgement calls made for data entries.
Include a Janno file
It is recommended that you include a janno file for the requested package to the PR.
While optional, recipes that include a janno file will be prioritised for processing.
.janno) for the requestedpackage.
.jannofile(s) matches the package name (i.e.packages/2023_my_package/2023_my_package.janno)..jannofile contains one record per poseidon_id specified in the SSF file.Recipe creation and validation
@delphis-bot create recipeto this pull request to awakenPoseidon's trusty helper. (This should be repeated whenever changes are
made to the SSF file contents).
After a few second, Delphis-bot will add a number of files to the PR.
Using the 'Files changed' tab, check that all of the following files were added:
packages/{package_name}/{package_name}.tsvwas added to the PR.packages/{package_name}/{package_name}.tsv_patch.shwas addedto the PR from template.
packages/{package_name}/script_versions.txtwas added to thePR.
packages/{package_name}/{package_name}.configwas added to thePR from template.
Additional configuration
Additional configuration may be required when processing the data through nf-core/eager.
If you think this may be the case here, please either leave a comment about it in the PR or
add the relevant parameters within the
paramssection at the end of the package config file.For example, if the published data from the paper have internal barcodes, please mention that
in a comment, or provide the relevant nf-core/eager parameters in the
paramssection.have commented so in this PR (or added the relevant parameters within the
paramssection at the end of the package config file).