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814 commits

Author SHA1 Message Date
sofstam
5b738ad353 Review + prettier 2023-01-31 09:35:40 +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
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
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 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
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
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 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
James Fellows Yates
2d64628552 Fix left-over warns from loca modules 2023-01-20 13:33:43 +01:00
Sofia Stamouli
7d4035d4c7
Add new line in the description of custom file 2023-01-19 13:44:10 +01:00
James A. Fellows Yates
d9003924be
Merge pull request #201 from genomic-medicine-sweden/removo_todo
Remove TODOs from test configs
2023-01-19 13:15:14 +01:00
James A. Fellows Yates
5162240e77
Merge pull request #208 from nf-core/post-usage-draft-tweaks
Post-release tweaks to usage.md
2023-01-19 11:09:54 +01:00
James A. Fellows Yates
36629b3dde
Merge branch 'dev' into post-usage-draft-tweaks 2023-01-19 10:36:59 +01:00
James A. Fellows Yates
49e4e20f84
Merge pull request #212 from nf-core/classification-v-profiling
Specify the difference between classification/profiling
2023-01-19 10:06:15 +01:00
James A. Fellows Yates
6e43695264
Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-01-19 08:55:23 +01:00
James A. Fellows Yates
6d380fbbff
Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-01-19 08:49:55 +01:00
Sofia Stamouli
4dcf8c0b02 Prettier 2023-01-17 15:50:10 +01:00
sofstam
024b683671 Update output and usage 2023-01-17 15:38:56 +01:00
James Fellows Yates
33d4a84237 Add explicit sentnece about classification/profiling 2023-01-17 15:23:59 +01:00
Sofia Stamouli
244fe5e30d
Merge branch 'nf-core:dev' into update_output 2023-01-17 14:47:56 +01:00
James A. Fellows Yates
0cda0d2c51
Merge pull request #213 from nf-core/multiqc-update
Updates MultiQC to 1.14 to add support for all our MQC modules!
2023-01-17 13:37:44 +01:00
James Fellows Yates
92dff9b453 Standardise file names using only underscore 2023-01-17 10:58:30 +01:00
James Fellows Yates
480248bcfd Deactivate all classifer columns from general stats 2023-01-17 10:33:35 +01:00
nf-core-bot
11400b016c [automated] Fix linting with Prettier 2023-01-16 14:11:18 +00:00
James Fellows Yates
0947e9b8ca Fix mOTUs issues 2023-01-16 15:09:30 +01:00
James Fellows Yates
c8f6d713a3 Add tool names to end of prefix files for easier distinguishing in general stats 2023-01-16 14:49:44 +01:00
James A. Fellows Yates
b34a021db7
Specify the difference between classification/profiling 2023-01-16 14:43:46 +01:00
James Fellows Yates
d6fa45b500 update MultiQC and include latest modules 2023-01-16 14:39:52 +01:00
Sofia Stamouli
06575b537d
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-16 12:59:23 +01:00
Sofia Stamouli
0e3f9f0b9a
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-16 12:59:13 +01:00
sofstam
9f21181972 Add documentation for output docs 2023-01-12 15:47:29 +01:00
Sofia Stamouli
3b6be07623
Merge branch 'nf-core:dev' into update_output 2023-01-11 16:56:18 +01:00
Sofia Stamouli
33bce738f5
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:50:06 +01:00
Sofia Stamouli
a49a907ad1
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:47:44 +01:00
Sofia Stamouli
953f9585c9
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:47:18 +01:00
Sofia Stamouli
719fc3cf5d
Update docs/output.md
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-01-11 16:46:30 +01:00
James A. Fellows Yates
6dcf619518
Merge pull request #209 from nf-core/module-version-bumps
Update all modules to make templaite compatible
2022-12-23 23:17:17 +01:00
James Fellows Yates
e5c6db96c8 update all modules to make templaite compatible 2022-12-23 17:23:05 +01:00
James Fellows Yates
ab0c62bdc1 Post-release tweaks to usage.md 2022-12-23 16:23:29 +01:00