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Author SHA1 Message Date
James Fellows Yates
16a3556bfc Changes after code review 2022-04-13 08:26:08 +02:00
James Fellows Yates
a15c45b00c Put map in the rigt place 2022-04-12 10:51:27 +02:00
James Fellows Yates
8d68914192 Re-add operator name 2022-04-12 10:47:44 +02:00
James Fellows Yates
26399718b2 Re-add pairment attachment 2022-04-12 10:46:03 +02:00
James Fellows Yates
2ef21c6ef3 Fix input to profiling 2022-04-12 10:14:05 +02:00
James Fellows Yates
9f221f84cc Only supply single input channel to profiling, as these are merged into single input channel at run_merging 2022-04-12 10:12:17 +02:00
James A. Fellows Yates
967b1f7d6e
Merge branch 'dev' into run-merging 2022-04-12 09:28:10 +02:00
James Fellows Yates
a5f4fc42d5 Fix run merging for unmerged PE data 2022-04-12 09:25:27 +02:00
James A. Fellows Yates
1ac5a129a8
Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory 
Delete extra unnecessary directory
 2022-04-11 20:46:50 +02:00
sofstam
989dc55ce1 Delete extra nf-core directory 2022-04-11 17:42:38 +02:00
James A. Fellows Yates
fb2f5ed73e
Merge pull request #50 from nf-core/docs-prelim 
Initial attempt at adding usage docs
 2022-04-11 10:52:18 +02:00
James A. Fellows Yates
b8b11fd065
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-11 10:30:29 +02:00
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
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