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972 commits 7 branches 0 tags 7.5 MiB
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119 commits

Author SHA1 Message Date
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +02:00
James Fellows Yates
21ae9d85c3 Ensure merge metaphlan3 tables happens on per database basis 2022-09-15 12:29:54 +02:00
James A. Fellows Yates
cc5df924e4
Merge branch 'dev' into module-update 2022-09-08 13:36:21 +02:00
James Fellows Yates
d11257b330 Module update 2022-09-08 08:08:36 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
James Fellows Yates
d4af88e3ff Make kaiju parameter clearer for documentation purpses and update documentation 2022-08-25 15:50:28 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00
James Fellows Yates
873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log 2022-07-29 09:51:34 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update 2022-07-28 15:48:59 +02:00
sofstam
cecbb41f88 Update centrifuge/kreport 2022-07-27 14:42:35 +02:00
James A. Fellows Yates
9d2be68fb8 Merge branch 'dev' into centrifuge_mqc 2022-07-26 18:01:30 +00:00
James A. Fellows Yates
1ef0975736 Merge branch 'dev' into porechop-log 2022-07-26 18:00:28 +00:00
James A. Fellows Yates
3054dea7c2 Get multiqc input working 2022-07-26 08:41:06 +00:00
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00
James Fellows Yates
139cf0d6aa Fix 2022-07-26 10:12:33 +02:00
James Fellows Yates
255afee4c7 Re-add the collects 2022-07-19 17:10:10 +02:00
Mahwash Jamy
811ded38af
Update subworkflows/local/profiling.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-19 16:44:48 +02:00
James A. Fellows Yates
8d7ddb5847
Apply suggestions from code review 2022-07-19 16:30:13 +02:00
mjamy
c4c82212e1 incorporate diamond log file into multiqc channel 2022-07-19 14:12:16 +02:00
James Fellows Yates
33a5402b25 Add emitting porechop logs to multiqc and fix collection of others 2022-07-19 13:50:39 +02:00
James A. Fellows Yates
c215ed5607
Merge branch 'dev' into motus/merge 2022-07-15 10:52:42 +02:00
James A. Fellows Yates
cc3967a3fd
Apply suggestions from code review 2022-07-15 10:51:41 +02:00
James Fellows Yates
31119f83c2 Send to MQC only the log file not the meta 2022-07-13 14:29:47 +02:00
James Fellows Yates
13280e2468 Fix .empty 2022-07-13 12:44:44 +02:00
James Fellows Yates
eaa69b65d8 Update mOTUs profile module and mix log for multiqc 2022-07-13 12:38:30 +02:00
James Fellows Yates
c22946cfab Fix motu versions not being exported if not run 2022-07-13 12:36:29 +02:00
James Fellows Yates
a0ee82bf43 Add motus/merge and biom support 2022-07-12 11:39:26 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus 2022-07-04 13:14:42 +02:00
Thomas A. Christensen II
6673ccf8d8
Update channel assignment alignment in profiling subworkflow 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-28 09:00:43 -05:00
Thomas A. Christensen II
4de43040a3
Switch to using raw classifications for Kaiju2Krona 2022-06-28 09:00:41 -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
JIANHONG OU
4b3216c1cb filter fasta inputs for mOTUs; 
fix the typo for nopreprocessing in nextflow.config.
 2022-05-24 08:42:18 -04:00
JIANHONG OU
68d0cc00fa add motus profile. 2022-05-23 08:05:06 -04:00
James Fellows Yates
87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 05:22:35 +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
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
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 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 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