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1009 commits

Author SHA1 Message Date
James Fellows Yates
b3837cce5b Relax strictness so can supply empty db_params but block if only single parameter with out ; 2023-02-08 15:44:37 +01:00
James Fellows Yates
fe3d42ffd7 Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters 2023-02-08 13:34:36 +01:00
James A. Fellows Yates
31d05d1994
Merge pull request #236 from nf-core/mapped-bam-fixes
Fix exporting of mapped/unmapped reads for consistency across both short and long reads
2023-02-07 18:42:18 +01:00
James Fellows Yates
18886c0cbc Start trying a different method with maps in profiling 2023-02-07 15:51:25 +01:00
James Fellows Yates
059cd17114 Fix exporting of mapped/unmapped reads for consistency across both short and long reads 2023-02-07 11:43:40 +01:00
James A. Fellows Yates
de5bdc36c5
Merge pull request #230 from genomic-medicine-sweden/documentation
Add documentation
2023-02-03 16:34:09 +01:00
sofstam
4123e06981 Apply last review suggestions 2023-02-03 15:54:29 +01:00
sofstam
3e2b181182 Apply review suggestions 2023-02-03 15:42:45 +01:00
Sofia Stamouli
ffc884b542
Merge branch 'nf-core:dev' into documentation 2023-02-03 15:22:51 +01:00
James A. Fellows Yates
2b40d809d8
Merge pull request #231 from nf-core/docs-t [skip ci]
Add warning about database parameters [skip ci]
2023-02-03 10:14:38 +01:00
James A. Fellows Yates
b4f88a29ce
Update docs/usage.md [skip ci] 2023-02-03 09:46:01 +01:00
James A. Fellows Yates
11a8624b39
Add warning about database parameters [skip ci] 2023-02-03 09:42:20 +01:00
sofstam
5363274867 Add some last documentation 2023-02-02 13:58:48 +01:00
James A. Fellows Yates
2e925e5b11
Merge pull request #229 from nf-core/full-test-profile-docs
Add full test data and documentation of the test data
2023-02-02 13:10:39 +01:00
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