James Fellows Yates
|
7ce55a99e8
|
Fix linting
|
2023-02-02 13:08:16 +01:00 |
|
James A. Fellows Yates
|
c4e366d47d
|
Add full test data and documentation of the test data
|
2023-02-02 11:59:26 +01:00 |
|
James A. Fellows Yates
|
a6b4e3c4d4
|
Merge pull request #225 from nf-core/output-docs-imporvements
Output Formatting tweaks
|
2023-01-31 13:25:07 +01:00 |
|
James Fellows Yates
|
932dc12fb1
|
Add list of expected tools in MultiQC report [skip ci]
|
2023-01-31 13:09:53 +01:00 |
|
James Fellows Yates
|
52907dcc26
|
Prettier
|
2023-01-31 13:07:07 +01:00 |
|
James A. Fellows Yates
|
d49344cefd
|
Merge pull request #228 from nf-core/bt2-error
Fix channel structure when supplying own host bt2 index
|
2023-01-31 13:03:53 +01:00 |
|
James Fellows Yates
|
225773000f
|
Fix channel structure when supplying own host bt2 index
|
2023-01-31 12:00:48 +01:00 |
|
James A. Fellows Yates
|
43a503096e
|
Merge pull request #227 from nf-core/mqc-update [skip ci]
Tweak MultiQC config [skip ci]
|
2023-01-31 11:11:52 +01:00 |
|
James Fellows Yates
|
01fca90496
|
Tweak MultiQC config [skip ci]
|
2023-01-31 11:08:46 +01:00 |
|
James A. Fellows Yates
|
b4d01ac226
|
Formatting tweaks
|
2023-01-31 10:23:36 +01:00 |
|
James A. Fellows Yates
|
f47c294931
|
Merge pull request #186 from genomic-medicine-sweden/update_output
Start the documentation of output.md
|
2023-01-31 09:58:54 +01:00 |
|
sofstam
|
366745bdbe
|
Prettier in usage
|
2023-01-31 09:38:43 +01:00 |
|
sofstam
|
5b738ad353
|
Review + prettier
|
2023-01-31 09:35:40 +01:00 |
|
James A. Fellows Yates
|
1d7da61801
|
Merge pull request #223 from nf-core/multiqc-tweaks
MultiQC Tweaks after full-test experiments
|
2023-01-30 11:25:28 +01:00 |
|
sofstam
|
0edef9ea57
|
Review suggestions + prettier
|
2023-01-30 11:16:18 +01:00 |
|
sofstam
|
bc2876228c
|
Apply review suggestions
|
2023-01-25 15:11:43 +01:00 |
|
James Fellows Yates
|
a77a437313
|
Triple patch combo!
|
2023-01-25 15:02:02 +01:00 |
|
James Fellows Yates
|
f63cec3473
|
Actually patch the patch
|
2023-01-25 14:58:19 +01:00 |
|
James Fellows Yates
|
d761edb615
|
Patch the patch
|
2023-01-25 14:55:57 +01:00 |
|
James A. Fellows Yates
|
47efd193cb
|
Merge pull request #219 from nf-core/allow-targz-motus [skip ci]
Allow all tool's databases to be provided as `.tar.gz` files
|
2023-01-25 13:48:43 +01:00 |
|
James A. Fellows Yates
|
2cbb56194a
|
Merge pull request #224 from nf-core/revert-metaphlan-nanopore-filter [skip ci]
Remove metaphlan3 nanopore filter as _sometimes_ it can work
|
2023-01-25 13:48:29 +01:00 |
|
James A. Fellows Yates
|
098ec087c9
|
Merge pull request #217 from nf-core/combine-kreports-fix [skip ci]
Dont fail on divide by 0 errors on centrifuge
|
2023-01-25 13:48:06 +01:00 |
|
sofstam
|
4f8ac72e1f
|
Add description of each tool
|
2023-01-25 13:25:33 +01:00 |
|
Sofia Stamouli
|
5d12785ca4
|
Merge branch 'nf-core:dev' into update_output
|
2023-01-25 09:47:30 +01:00 |
|
James A. Fellows Yates
|
4289e1f901
|
Remove metaphlan3 nanopore filter as _sometimes_ it can work
|
2023-01-24 15:42:14 +01:00 |
|
James Fellows Yates
|
7843665544
|
Link rather than mv
|
2023-01-24 15:32:49 +01:00 |
|
James A. Fellows Yates
|
c765b3f0bc
|
Merge branch 'dev' into allow-targz-motus
|
2023-01-24 15:20:29 +01:00 |
|
James Fellows Yates
|
f940b07dfe
|
Remove changes from other PR
|
2023-01-24 15:15:02 +01:00 |
|
James Fellows Yates
|
bdbb111344
|
Turn off all profilers in generla stats
|
2023-01-24 15:08:28 +01:00 |
|
James Fellows Yates
|
a993300099
|
Tweaks to MultiQC based on full test experiments
|
2023-01-24 15:06:42 +01:00 |
|
Moritz E. Beber
|
2431bddcbc
|
Merge pull request #222 from nf-core/fix-save-minimap2
fix: correct pattern to publish minimap2 index
|
2023-01-24 14:57:46 +01:00 |
|
James Fellows Yates
|
e7d7affcd0
|
Pick up Kraken2 files correctly
|
2023-01-24 14:44:14 +01:00 |
|
James A. Fellows Yates
|
00178d3431
|
Merge pull request #221 from nf-core/metaphlan3-filter-nanopore
Filter out nanopore data prior Metaphlan3
|
2023-01-24 14:39:02 +01:00 |
|
Moritz E. Beber
|
40f1e7b27a
|
fix: correct pattern to publish minimap2 index
|
2023-01-24 14:15:51 +01:00 |
|
James Fellows Yates
|
14826d5205
|
Separate conditions, remove some left-over dumps
|
2023-01-24 13:20:58 +01:00 |
|
James Fellows Yates
|
0358489be0
|
Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified
|
2023-01-24 13:05:52 +01:00 |
|
James A. Fellows Yates
|
6eafcc6499
|
Try Moritz's trick, assuming validate_db_rows already checks for tool name validity
|
2023-01-24 12:43:34 +01:00 |
|
James A. Fellows Yates
|
38cbfe9a1c
|
Merge pull request #220 from nf-core/sr-lr-guidance
Add comment about recommendation to split SR/LR
|
2023-01-24 11:51:18 +01:00 |
|
James A. Fellows Yates
|
9cf2d8763f
|
[skip ci] Update docs/usage.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
|
2023-01-24 11:50:58 +01:00 |
|
James Fellows Yates
|
4df3409f4a
|
Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus
|
2023-01-24 11:50:28 +01:00 |
|
James Fellows Yates
|
9205831273
|
Start adding filter for long read and MP3
|
2023-01-24 11:50:10 +01:00 |
|
James A. Fellows Yates
|
03ef6a69f8
|
Merge pull request #215 from nf-core/remove-platform-specificity
Remove platform specificity for MALT
|
2023-01-24 11:47:48 +01:00 |
|
James Fellows Yates
|
085d9e519c
|
[skip ci] add comment about recommendation to split SR/LR
|
2023-01-24 11:39:37 +01:00 |
|
James Fellows Yates
|
2439aa69d0
|
Use specific samplesheet for MALT without LR reads due to GHA memory limits
|
2023-01-24 10:58:03 +01:00 |
|
James Fellows Yates
|
1a148c5d49
|
Remove double If and format for readability
|
2023-01-24 10:48:23 +01:00 |
|
James A. Fellows Yates
|
d56e3133f9
|
Allow databases of all tools to arrive as tar.gz
|
2023-01-24 10:45:01 +01:00 |
|
James Fellows Yates
|
1c820f21b3
|
Dont fail on divide by 0 errors on centrifuge
|
2023-01-20 17:53:55 +01:00 |
|
James A. Fellows Yates
|
d3bad1d720
|
Merge pull request #214 from nf-core/local-module-template-sync
Sync local modules with latest template module structure
|
2023-01-20 14:41:11 +01:00 |
|
James Fellows Yates
|
606ffc0eb1
|
Remove platform specificity for MALT
|
2023-01-20 13:40:59 +01:00 |
|
James Fellows Yates
|
cac6f54d2d
|
[extra] Fix warn related to recently changed parameter
|
2023-01-20 13:36:17 +01:00 |
|