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Author SHA1 Message Date
James Fellows Yates
457c13e8b7 Add additional tips for host removal 2022-04-17 17:55:23 +02:00
James Fellows Yates
818d3bd053 Complete documentation for preprocessing subworkflows 2022-04-17 17:53:22 +02:00
James Fellows Yates
d0256ec937 Prettier 2022-04-16 07:45:24 +02:00
James Fellows Yates
cc73cdd51d Add generation of taxon-table like output for MALT 2022-04-16 07:42:30 +02:00
James A. Fellows Yates
6fecb3eeb7
Merge pull request #54 from nf-core/dev 
Get upstream changes
 2022-04-16 06:17:33 +02:00
sofstam
0e5c9e7bdd Type:boolean for kaiju in nextflow_schema.json 2022-04-14 09:14:05 +02:00
sofstam
6736a2a980 Update README.md, nextflow_schema.json 2022-04-13 19:00:52 +02:00
sofstam
68ce5843a4 Add kaiju in taxprofiler 2022-04-13 18:51:56 +02:00
James A. Fellows Yates
fc8a83245a
Add short-read host removal via BowTie2 alignment mapping 
Add short-read host removal via BowTie2 alignment mapping
 2022-04-13 15:29:16 +02:00
James A. Fellows Yates
5e80df0f94
Apply suggestions from code review 2022-04-13 15:27:53 +02:00
James Fellows Yates
aa2d07c42a Fix merge cockup 2022-04-13 14:19:19 +02:00
James A. Fellows Yates
70f94603b0
Merge branch 'dev' into hostremoval 2022-04-13 13:59:51 +02:00
James A. Fellows Yates
67d94a9a8d
Merge pull request #45 from nf-core/run-merging 
Re-add run merging
 2022-04-13 12:27:37 +02:00
James Fellows Yates
dfeaa0d1fe Rename subworkflow parameters for consistency 2022-04-13 12:00:28 +02:00
James Fellows Yates
de57340526 Start work 2022-04-13 11:49:35 +02:00
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 Fellows Yates
78182c2a8c Add comma 2022-04-11 13:40:24 +02:00
James Fellows Yates
ff2e508a38 Merge branch 'hostremoval' of github.com:nf-core/taxprofiler into hostremoval 2022-04-11 13:38:53 +02:00
James Fellows Yates
29073e3c93 Update CI tests 2022-04-11 13:38:42 +02:00
James A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +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