diff --git a/.github/assets/adaptivecard.json b/.github/assets/adaptivecard.json
deleted file mode 100644
index c0e60fe..0000000
--- a/.github/assets/adaptivecard.json
+++ /dev/null
@@ -1,67 +0,0 @@
-{
- "type": "message",
- "attachments": [
- {
- "contentType": "application/vnd.microsoft.card.adaptive",
- "contentUrl": null,
- "content": {
- "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
- "msteams": {
- "width": "Full"
- },
- "type": "AdaptiveCard",
- "version": "1.2",
- "body": [
- {
- "type": "TextBlock",
- "size": "Large",
- "weight": "Bolder",
- "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
- "text": "sanger-tol/ascc v${version} - ${runName}",
- "wrap": true
- },
- {
- "type": "TextBlock",
- "spacing": "None",
- "text": "Completed at ${dateComplete} (duration: ${duration})",
- "isSubtle": true,
- "wrap": true
- },
- {
- "type": "TextBlock",
- "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
- "wrap": true
- },
- {
- "type": "TextBlock",
- "text": "The command used to launch the workflow was as follows:",
- "wrap": true
- },
- {
- "type": "TextBlock",
- "text": "${commandLine}",
- "isSubtle": true,
- "wrap": true
- }
- ],
- "actions": [
- {
- "type": "Action.ShowCard",
- "title": "Pipeline Configuration",
- "card": {
- "type": "AdaptiveCard",
- "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
- "body": [
- {
- "type": "FactSet",
- "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
- ]
- }
- ]
- }
- }
- ]
- }
- }
- ]
-}
diff --git a/.github/assets/email_template.html b/.github/assets/email_template.html
deleted file mode 100644
index 1492d1e..0000000
--- a/.github/assets/email_template.html
+++ /dev/null
@@ -1,53 +0,0 @@
-
-
-
-
-
-
-
- sanger-tol/ascc Pipeline Report
-
-
-
-
-
-
-
sanger-tol/ascc v${version}
-
Run Name: $runName
-
-<% if (!success){
- out << """
-
-
sanger-tol/ascc execution completed unsuccessfully!
-
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
-
The full error message was:
-
${errorReport}
-
- """
-} else {
- out << """
-
- sanger-tol/ascc execution completed successfully!
-
- """
-}
-%>
-
-
The workflow was completed at $dateComplete (duration: $duration)
-
The command used to launch the workflow was as follows:
-
$commandLine
-
-
Pipeline Configuration:
-
-
- <% out << summary.collect{ k,v -> "| $k | $v |
|---|
" }.join("\n") %>
-
-
-
-
sanger-tol/ascc
-
https://github.com/sanger-tol/ascc
-
-
Methods
- Data was processed using sanger-tol/ascc v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
- The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:
- ${workflow.commandLine}
- ${tool_citations}
- References
-
- - Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- - Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- - Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- - da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
- ${tool_bibliography}
-
-
-
Notes:
-
- ${nodoi_text}
- - The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- - You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
-
-