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
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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
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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
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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
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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
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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
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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
James Fellows Yates
a76576c16b
Prettier
2022-04-03 17:24:50 +02:00
James A. Fellows Yates
b2e29ea23a
Merge branch 'dev' into hostremoval
2022-04-03 17:24:07 +02:00
James Fellows Yates
066ceb2bca
Remove flagstat as bowtie2 reports this itself
2022-04-03 17:23:14 +02:00
Moritz E. Beber
fe628b3578
Merge pull request #29 from nf-core/add-metaphlan
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Add metaphlan3
2022-04-03 09:08:01 +02:00
James Fellows Yates
482112bb42
Start work on host removal
2022-04-03 07:58:40 +02:00
James Fellows Yates
d3572e1878
Final MQC fix for AR2 (remove too-early collect)
2022-04-03 07:28:01 +02:00
Moritz E. Beber
f5baf910be
Apply suggestions from code review
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-03 00:21:09 +02:00
Moritz E. Beber
be93eae640
fix: insert .fastq
file extension
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The MetaPhlAn3 module computes the input type from the file extension
without the possibility to configure an override. Since AdapterRemoval2
creates files without `.fastq` extensions, MetaPhlAn3 input was determined
to be SAM.
2022-04-02 21:50:13 +02:00