James Fellows Yates
|
b892fd0be5
|
Initial attempt at docs
|
2022-04-10 22:17:44 +02:00 |
|
James A. Fellows Yates
|
dd22e042be
|
Merge pull request #47 from nf-core/profiling-subworkflow
Move profiling to subworkflow
|
2022-04-10 16:54:35 +02:00 |
|
James Fellows Yates
|
030099c559
|
A bit of clean up
|
2022-04-10 07:26:20 +02:00 |
|
James Fellows Yates
|
80c08af11b
|
Mix in profiling versions into mainline versons channel
|
2022-04-10 06:48:25 +02:00 |
|
James Fellows Yates
|
082093f3de
|
Prettier
|
2022-04-10 06:44:10 +02:00 |
|
James Fellows Yates
|
ecf0eea4f9
|
Move profiling to subworkflow and standardise outputs
|
2022-04-10 06:43:30 +02:00 |
|
James Fellows Yates
|
afb66e445f
|
Append pairment to ID at profiling to prevent multiqc-level filename crash
|
2022-04-08 21:36:59 +02:00 |
|
James Fellows Yates
|
8839fe22b8
|
Fix output tuple for reads
|
2022-04-08 20:02:22 +02:00 |
|
James Fellows Yates
|
35cb6e042a
|
Flatten the right thing
|
2022-04-08 13:46:12 +02:00 |
|
James Fellows Yates
|
6c14f2b230
|
Remove the flattening?
|
2022-04-08 13:44:52 +02:00 |
|
James Fellows Yates
|
a634814d84
|
Formatting and fix fastp output
|
2022-04-08 13:34:00 +02:00 |
|
James Fellows Yates
|
ca011ccc5b
|
Fix cat_fastq naming logic?
|
2022-04-08 13:28:37 +02:00 |
|
James Fellows Yates
|
d130a72d74
|
Get this working
|
2022-04-08 13:09:23 +02:00 |
|
James Fellows Yates
|
4d726a87e9
|
Fix metadata removal
|
2022-04-08 12:01:07 +02:00 |
|
James Fellows Yates
|
74c496f6af
|
Fix CAT_FASTQ output
|
2022-04-08 11:58:16 +02:00 |
|
James Fellows Yates
|
7b08c49cd6
|
Re-add run merging and gonna let GHA see if it works >.>
|
2022-04-08 11:54:54 +02:00 |
|
Sofia Stamouli
|
5f24f94391
|
Merge pull request #31 from genomic-medicine-sweden/classification_centrifuge
Add centrifuge classification (centrifuge/centrifuge module)
|
2022-04-08 11:26:57 +02:00 |
|
Sofia Stamouli
|
63bc597daf
|
Prettier
|
2022-04-08 11:01:45 +02:00 |
|
Sofia Stamouli
|
fd5ebea9a6
|
Remove old centrifuge module
|
2022-04-08 10:57:58 +02:00 |
|
Sofia Stamouli
|
48d28cf8d4
|
Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-04-08 10:00:10 +02:00 |
|
Sofia Stamouli
|
2dfe3b3cc1
|
Update conf/test.config
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
|
2022-04-08 10:00:04 +02:00 |
|
Sofia Stamouli
|
3d45ac57ae
|
Prettier
|
2022-04-07 16:42:22 +02:00 |
|
sofstam
|
26779a4420
|
Remove db_name from nextflow.config
|
2022-04-07 16:27:19 +02:00 |
|
sofstam
|
606e5da7d5
|
Check if PR works with centrifuge/centrifuge module
|
2022-04-07 16:13:17 +02:00 |
|
James A. Fellows Yates
|
b554aa3e4d
|
Merge branch 'dev' into hostremoval
|
2022-04-07 14:00:10 +02:00 |
|
James A. Fellows Yates
|
4c4475c316
|
Merge pull request #43 from nf-core/refactor-config
Refactor config
|
2022-04-06 11:03:45 +02:00 |
|
Moritz E. Beber
|
7ab3aa546b
|
refactor: use flags to publish reads
|
2022-04-06 10:27:11 +02:00 |
|
Moritz E. Beber
|
018b9a8ea6
|
refactor: do not generally publish output
|
2022-04-06 10:21:43 +02:00 |
|
Moritz E. Beber
|
8827b143a2
|
fix: disable publishing correctly
|
2022-04-05 20:56:19 +02:00 |
|
Moritz E. Beber
|
af12435fa5
|
fix: use parameter for publish mode everywhere
|
2022-04-05 20:56:19 +02:00 |
|
Moritz E. Beber
|
c40a9a0011
|
refactor: avoid publishing unpacked databases
|
2022-04-05 20:54:32 +02:00 |
|
James A. Fellows Yates
|
e72be724a6
|
Merge pull request #36 from nf-core/complexity-filter-bbduk
Add bbduk and prinseq complexity (entropy or dust-based) short read filtering
|
2022-04-05 16:45:40 +02:00 |
|
James Fellows Yates
|
82aa89ad63
|
re add missing switch meta of merged reads to true
|
2022-04-05 13:55:11 +02:00 |
|
James Fellows Yates
|
98f082d7b6
|
Fix mistake in previous upstream merge with AR2 output channel for settings file
|
2022-04-05 13:17:54 +02:00 |
|
James Fellows Yates
|
4dbd0ddc73
|
Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk
|
2022-04-05 13:14:13 +02:00 |
|
James Fellows Yates
|
5b9355725d
|
Whoops
|
2022-04-05 13:14:06 +02:00 |
|
James A. Fellows Yates
|
23fb319779
|
Merge branch 'dev' into complexity-filter-bbduk
|
2022-04-05 13:11:15 +02:00 |
|
James Fellows Yates
|
245a4d1f5d
|
Fix MQC staging and remove debugging dump
|
2022-04-05 13:08:44 +02:00 |
|
Moritz E. Beber
|
b37a9c5576
|
Merge pull request #42 from nf-core/refactor-adapterremoval
Refactor adapterremoval
|
2022-04-05 12:04:36 +02:00 |
|
Moritz E. Beber
|
39e5e802c7
|
refactor: make code more explicit, add comment
|
2022-04-05 11:29:39 +02:00 |
|
Moritz E. Beber
|
59b2088aa1
|
style: apply prettier
|
2022-04-05 11:16:43 +02:00 |
|
James Fellows Yates
|
d46ddd972c
|
Expand tests and fix schema after review
|
2022-04-05 11:04:30 +02:00 |
|
Moritz E. Beber
|
0e9b2989e3
|
refactor: remove superfluous ENSURE_FASTQ_EXTENSION
|
2022-04-05 10:53:04 +02:00 |
|
Moritz E. Beber
|
c54c32c494
|
chore: update adapterremoval
|
2022-04-05 10:18:34 +02:00 |
|
James Fellows Yates
|
bb6dd738bd
|
Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk
|
2022-04-04 21:21:34 +02:00 |
|
James Fellows Yates
|
613f6a5565
|
Prettier
|
2022-04-04 21:21:29 +02:00 |
|
James A. Fellows Yates
|
3d662d2e06
|
Merge branch 'dev' into complexity-filter-bbduk
|
2022-04-04 21:19:36 +02:00 |
|
James Fellows Yates
|
a384162810
|
Add prinseq as alternative complexity filtering
|
2022-04-04 21:16:51 +02:00 |
|
sofstam
|
3a56206513
|
Centrifuge classification
|
2022-04-04 16:55:48 +02:00 |
|
sofstam
|
d897c922b2
|
Add centrifuge classificatioN
|
2022-04-04 13:51:51 +02:00 |
|