Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Patch release: 1.1.6 #469

Merged
merged 65 commits into from
Apr 16, 2024
Merged
Changes from 1 commit
Commits
Show all changes
65 commits
Select commit Hold shift + click to select a range
c2a15e2
Apply review suggestions
sofstam Feb 8, 2024
444d323
Merge branch 'nf-core:dev' into dev
sofstam Feb 8, 2024
154a219
Bump to new dev version
sofstam Feb 8, 2024
e04e613
Prettier
sofstam Feb 8, 2024
7a86d96
Update CHANGELOG.md
sofstam Feb 8, 2024
32a5539
Merge pull request #447 from genomic-medicine-sweden/bump_version
sofstam Feb 8, 2024
1041602
Template update for nf-core/tools version 2.13
nf-core-bot Feb 20, 2024
9f33175
make full-pathed SVGs rather than text versions of the logos
jfy133 Feb 28, 2024
c3128c6
Include font-fullpath metromap
jfy133 Feb 28, 2024
53439cb
Template update for nf-core/tools version 2.13.1
nf-core-bot Feb 29, 2024
b12a0bd
update the template and add nf-validation
LilyAnderssonLee Mar 1, 2024
0310d75
remove custom_dumpsoftwareversions
LilyAnderssonLee Mar 1, 2024
1c515f5
Update .github/workflows/ci.yml
LilyAnderssonLee Mar 1, 2024
d5e6133
Update ci.yml
sofstam Mar 1, 2024
132a734
update error message in schema_databases.json
LilyAnderssonLee Mar 4, 2024
5516e87
Update the db_path format definition to include both options for file…
LilyAnderssonLee Mar 4, 2024
7f9d873
Update main.nf
LilyAnderssonLee Mar 5, 2024
af065d8
Update assets/schema_database.json
LilyAnderssonLee Mar 5, 2024
9389c31
Update assets/schema_database.json
LilyAnderssonLee Mar 5, 2024
596708b
Update assets/schema_database.json
LilyAnderssonLee Mar 5, 2024
b730faa
update db_params in schema_databases.json
LilyAnderssonLee Mar 5, 2024
c1e09b5
Update taxprofiler.nf
LilyAnderssonLee Mar 6, 2024
bfe9aa8
Update taxprofiler.nf
LilyAnderssonLee Mar 6, 2024
54640ea
Update taxprofiler.nf
LilyAnderssonLee Mar 6, 2024
e81f171
Merge pull request #454 from nf-core/nf-core-template-merge-2.13.1
LilyAnderssonLee Mar 6, 2024
b90a05c
Merge branch 'dev' of github.com:nf-core/taxprofiler into logo-fix
jfy133 Mar 14, 2024
91f61ea
Merge pull request #453 from nf-core/logo-fix
jfy133 Mar 14, 2024
1b3ce6b
correct nanopore and fasta input channel
LilyAnderssonLee Mar 18, 2024
9213006
Merge pull request #459 from LilyAnderssonLee/fix-validation-dev
maxulysse Mar 18, 2024
4d6e111
Try adding nextflow strict
jfy133 Mar 21, 2024
aaf6d62
Start fixing untar MALT db error
jfy133 Mar 21, 2024
7f82975
update nf-validation and turn off kaiju2krona output
LilyAnderssonLee Mar 21, 2024
d8f136d
Optimise database untarring and prevent publishing clashses
jfy133 Mar 21, 2024
c099269
Update changelog
jfy133 Mar 21, 2024
d697e6a
Merge pull request #463 from LilyAnderssonLee/update-validation
LilyAnderssonLee Mar 21, 2024
28c250e
Update changelog
jfy133 Mar 21, 2024
c5b112d
Add nf-validation specific parameter to ignore list
jfy133 Mar 21, 2024
06d7ecf
Remove a debugging dump
jfy133 Mar 22, 2024
b527a85
Remove final dump
jfy133 Mar 22, 2024
e6097e6
Actually remove it
jfy133 Mar 22, 2024
4dc0900
Fix occasional split errors, due to db_params replacement not actuall…
jfy133 Mar 28, 2024
630a25c
Update workflows/taxprofiler.nf
jfy133 Mar 28, 2024
1b4c5f0
Add option to save uncompressed databases, turn
jfy133 Apr 4, 2024
54a6cd7
Apply suggestions from code review
jfy133 Apr 4, 2024
968ae64
[automated] Fix code linting
nf-core-bot Apr 4, 2024
f894a4b
Update CHANGELOG.md
jfy133 Apr 4, 2024
2ebce4c
Update nextflow_schema.json
jfy133 Apr 4, 2024
593c013
Merge pull request #461 from nf-core/nextflow-enable-strict
jfy133 Apr 4, 2024
c6134cc
chore: avoid mOTUs download progress report
Midnighter Mar 27, 2024
f7caedc
fix: transform channels to combine on DB name
Midnighter Mar 27, 2024
3d30547
refactor: extraction function to group profiles
Midnighter Mar 27, 2024
2c430aa
docs: add changelog entry
Midnighter Mar 27, 2024
46e6637
fix: correct file name for combined kraken2 reports
Midnighter Apr 6, 2024
399b87c
chore: remove channel dumps used for debugging
Midnighter Apr 7, 2024
a9afbc0
Merge pull request #464 from nf-core/fix-combine
Midnighter Apr 7, 2024
eaaa9f2
bump the version
LilyAnderssonLee Apr 11, 2024
bf48a1c
Merge pull request #468 from LilyAnderssonLee/bump_version
LilyAnderssonLee Apr 11, 2024
04a2ba7
update download-pipeline.yml
LilyAnderssonLee Apr 12, 2024
06d2985
update download-pipeline.yml
LilyAnderssonLee Apr 12, 2024
89d4ca6
Merge pull request #470 from LilyAnderssonLee/fix-download-pipeline
LilyAnderssonLee Apr 12, 2024
8941b6e
manully define stub run branch is master
LilyAnderssonLee Apr 12, 2024
2db93e4
update changelog and remove disk clean in download_pipeline.yml
LilyAnderssonLee Apr 12, 2024
39a66a3
Update download_pipeline.yml
LilyAnderssonLee Apr 12, 2024
8fe3968
remove stub run in download pipeline
LilyAnderssonLee Apr 16, 2024
e805e26
Merge pull request #471 from LilyAnderssonLee/download-pipeline-bug
jfy133 Apr 16, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
Update assets/schema_database.json
Co-authored-by: Matthias Hörtenhuber <[email protected]>
LilyAnderssonLee and mashehu authored Mar 5, 2024

Verified

This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
commit 9389c31646eb71377638df0c409328276510df84
2 changes: 1 addition & 1 deletion assets/schema_database.json
Original file line number Diff line number Diff line change
@@ -44,7 +44,7 @@
"not": {
"pattern": ".*;"
},
"errorMessage": "Invalid database db_params entry. Bracken requires a semi-colon if passing parameter."
"errorMessage": "Invalid database db_params entry. Bracken requires a semi-colon for passing one or more parameters."
},
{
"properties": {