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306 commits 7 branches 0 tags 7.5 MiB
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105 commits

Author SHA1 Message Date
Thomas A. Christensen II
fa87975983
Add Krona creation and formatting to PROFILING subworkflow 2022-06-14 10:34:35 -05:00
James Fellows Yates
e0ad49ebc9 Fix metadata manipulaton for malt 2022-06-10 19:33:37 +02:00
James A. Fellows Yates
621b6a3d09
Add comments about MALT id replacement and refactor for simplicity 2022-06-10 11:27:51 +02:00
James A. Fellows Yates
ebdd5683b2
Apply suggestions from code review 2022-06-03 22:33:48 +02:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads 2022-06-03 13:48:54 +02:00
James A. Fellows Yates
c9581b1796
Merge branch 'dev' into support-aligned-reads 2022-06-02 12:45:29 +02:00
James Fellows Yates
310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong 2022-05-31 13:05:52 +02:00
James Fellows Yates
47a5ae0cff Add FASTP complexity option 2022-05-07 06:09:05 +02:00
James Fellows Yates
87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 05:22:35 +02:00
James A. Fellows Yates
e7b54801ed
Merge pull request #75 from nf-core/improve-error-message 
Only create profiler input channels when profiler activated
 2022-05-06 11:51:33 +02:00
ljmesi
5e6be52fab Implement hostremoval 2022-05-03 09:34:27 +02:00
James Fellows Yates
d5049a34e4 Add missing close bracket 2022-05-01 07:28:29 +02:00
James Fellows Yates
4094706421 Only create profiler input channels when profiler activate 2022-05-01 07:24:58 +02:00
James Fellows Yates
031cb45934 Add initial longread QC filtering - requires filtlong module update 2022-05-01 07:18:14 +02:00
James Fellows Yates
8126d16dee Add draft version of DIAMOND 2022-04-29 21:59:42 +02:00
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
James A. Fellows Yates
bc84afe80d
Merge pull request #66 from nf-core/versions-fix 
Fix version reporting
 2022-04-25 16:38:28 +02:00
James Fellows Yates
06b38f3699 Fix crash, add missing versions 2022-04-23 08:36:01 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
Sofia Stamouli
e71e7b86a2
Merge pull request #53 from genomic-medicine-sweden/classification_kaiju 
Add kaiju/kaiju in taxprofiler
 2022-04-20 10:57:00 +02:00
Sofia Stamouli
236141f065 Resolve conflicts with dev 2022-04-20 10:17:10 +02:00
James A. Fellows Yates
571495c812
Merge pull request #60 from nf-core/fasta-filtering 
Adds filtering out of FASTA for tools that don't support it
 2022-04-20 10:11:17 +02:00
James Fellows Yates
9fd94b1389 Switch to string interpolation 2022-04-20 09:25:54 +02:00
James Fellows Yates
60d232d62c Revert "Update subworkflows/local/profiling.nf" 
This reverts commit b7d0557ee0.
 2022-04-20 09:23:38 +02:00
James A. Fellows Yates
b7d0557ee0
Update subworkflows/local/profiling.nf 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-20 09:15:45 +02:00
James A. Fellows Yates
87777a4289
Update subworkflows/local/profiling.nf 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-19 12:54:57 +02:00
James A. Fellows Yates
ecaff371aa
Update input_check.nf 2022-04-18 07:35:19 +02:00
James A. Fellows Yates
9f634805e4
Update subworkflows/local/profiling.nf 2022-04-18 07:31:44 +02:00
James A. Fellows Yates
9c3c8f1f4e
Merge branch 'dev' into fasta-filtering 2022-04-18 07:31:14 +02:00
James Fellows Yates
6307a9cf43 Typos 2022-04-18 07:28:09 +02:00
James Fellows Yates
491c2d8949 Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages." 
This reverts commit 564474cafe.
 2022-04-18 07:26:15 +02:00
James Fellows Yates
564474cafe Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages. 2022-04-18 07:21:12 +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
68ce5843a4 Add kaiju in taxprofiler 2022-04-13 18:51:56 +02:00
James A. Fellows Yates
70f94603b0
Merge branch 'dev' into hostremoval 2022-04-13 13:59:51 +02:00
James Fellows Yates
de57340526 Start work 2022-04-13 11:49:35 +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 A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +02:00
James Fellows Yates
030099c559 A bit of clean up 2022-04-10 07:26:20 +02:00
James Fellows Yates
ecf0eea4f9 Move profiling to subworkflow and standardise outputs 2022-04-10 06:43:30 +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