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Author SHA1 Message Date
James Fellows Yates
cda1274918 Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile 2022-04-23 06:47:59 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
James A. Fellows Yates
63230c3254
Merge pull request #63 from nf-core/maxforks 
Update test.config to only allow maxFork to 1 for MALT_RUN
 2022-04-21 12:57:37 +02:00
James A. Fellows Yates
47a34d4c7e
Merge pull request #59 from nf-core/hostremoval-publish-fix 
Add finer control over for hostremoval saving
 2022-04-21 12:57:09 +02:00
James A. Fellows Yates
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +02:00
James A. Fellows Yates
d850333e11
Linting 2022-04-20 13:42:26 +02:00
James A. Fellows Yates
d031322c16
Update test.config 2022-04-20 13:41:01 +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 A. Fellows Yates
d16cd75652
Merge branch 'dev' into hostremoval-publish-fix 2022-04-20 09:53:51 +02:00
James A. Fellows Yates
53d76559af
Merge pull request #55 from nf-core/megan-postprocessing 
Add MEGAN for MALT postprocessing
 2022-04-20 09:52:55 +02:00
James A. Fellows Yates
fb5347a9fc
Merge pull request #58 from nf-core/docs 
Add documentation for preprocessing subworkflows
 2022-04-20 09:26:53 +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
ac714dd30f
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-20 09:22:10 +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
Sofia Stamouli
4e1b1269be Apply prettier 2022-04-19 13:11:43 +02:00
Sofia Stamouli
dc276e8bae
Merge branch 'nf-core:dev' into classification_kaiju 2022-04-19 13:09:15 +02:00
sofstam
1b7ff2265d Update usage.md, reformat test.config and modules.config 2022-04-19 13:04:58 +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
9880baa0b8 Get build directory working 2022-04-18 06:37:23 +02:00
James Fellows Yates
b036ed5b73 Prettier 2022-04-17 22:28:18 +02:00
James Fellows Yates
2cfcdf2dd2 Add finer controler over for hostremoval saving 2022-04-17 22:27:04 +02:00
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