1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-11 02:43:09 +00:00
Commit graph

957 commits

Author SHA1 Message Date
Sofia Stamouli
7e7299203c
Set values to false 2022-12-02 08:55:23 +01:00
sofstam
6d140c683a Merge branch 'dev' into update_motus 2022-12-01 18:49:23 +01:00
James A. Fellows Yates
80c25008d0
Merge pull request #177 from nf-core/sep-krakenuniq-test
Separate KrakenUniq test run
2022-12-01 17:34:30 +01:00
nf-core-bot
410196c37b [automated] Fix linting with Prettier 2022-12-01 14:33:34 +00:00
sofstam
4800a5f03e Update schema 2022-12-01 14:23:40 +01:00
James A. Fellows Yates
a34b240dfc
Merge pull request #174 from nf-core/malt-update
Update MALT
2022-12-01 13:58:30 +01:00
James Fellows Yates
f960c14caf Fix typos 2022-12-01 13:46:57 +01:00
sofstam
38a818fd17 Apply review suggestions 2022-12-01 13:42:21 +01:00
James A. Fellows Yates
ef1d2da179
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-12-01 12:53:34 +01:00
sofstam
1965ade961 Update schema 2022-12-01 11:32:51 +01:00
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +01:00
James Fellows Yates
bc98f5b80f Separate KrakenUniq test run 2022-12-01 10:37:14 +01:00
nf-core-bot
8067012c01 [automated] Fix linting with Prettier 2022-12-01 09:15:35 +00:00
James A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
2022-12-01 09:03:29 +01:00
sofstam
933b820c19 Apply review suggestions 2022-11-29 16:57:07 +01:00
Sofia Stamouli
e85c75dcba
Merge branch 'dev' into update_motus 2022-11-29 15:12:31 +01:00
sofstam
12dd836e9c Fix conflict 2022-11-29 15:00:27 +01:00
sofstam
f389029848 Fix merge conflic 2022-11-29 14:38:39 +01:00
James Fellows Yates
d7fbe55849 Add KU to the test profiles and add id to KU processes 2022-11-29 14:19:01 +01:00
Sofia Stamouli
7e3ece53bd
Update modules.config 2022-11-29 13:31:00 +01:00
Sofia Stamouli
0088b07220
Fix trailing whitespace 2022-11-29 13:28:04 +01:00
James A. Fellows Yates
770a35d7ac
Update conf/modules.config 2022-11-29 12:49:20 +01:00
Sofia Stamouli
ba727a81ae Fix left-padding spaces 2022-11-29 12:45:14 +01:00
Sofia Stamouli
71b52b9c94 Apply review suggestions 2022-11-29 11:58:23 +01:00
James A. Fellows Yates
3d949a803f
Merge pull request #175 from nf-core/schema-clean
Fix schema location ofr fastqc/falco option
2022-11-29 11:49:27 +01:00
Sofia Stamouli
fb6be69d7e Prettier should work now 2022-11-29 11:37:20 +01:00
sofstam
644a29c699 Prettier 2022-11-29 11:34:57 +01:00
sofstam
5254b8d679 Prettier 2022-11-29 11:25:52 +01:00
sofstam
0235ef42ca Update nextflow_schema.json 2022-11-29 11:15:40 +01:00
sofstam
49af33f68e Include NCBI_id, read counts and mgc arguments in motus 2022-11-29 11:07:29 +01:00
Moritz E. Beber
af8ce2cbfd chore: update krakenuniq 2022-11-29 10:27:35 +01:00
James Fellows Yates
d6c0ebb4c6 Prettier 2022-11-29 10:14:33 +01:00
Moritz E. Beber
ddcf38de22 refactor: make mappings explicit 2022-11-29 10:14:20 +01:00
James Fellows Yates
f13185d98b Fix schema location ofr fastqc/falco option 2022-11-29 10:13:46 +01:00
James A. Fellows Yates
f114cc4122
Apply suggestions from code review 2022-11-24 16:55:19 +01:00
James A. Fellows Yates
17b1e3df1c
Update test.config 2022-11-24 16:53:39 +01:00
James Fellows Yates
a20b3e3c58 Try to reduce MALT memory 2022-11-24 15:51:12 +01:00
James Fellows Yates
131b39aa8b Fix linting 2022-11-24 15:49:06 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
Sofia Stamouli
f8b769a8f0
Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats
Include the mapped reads in samtools stats
2022-11-23 10:21:47 +01:00
sofstam
481f90589c Apply review suggestions 2022-11-23 09:08:22 +01:00
Moritz E. Beber
b6f5930b49
Merge pull request #171 from nf-core/chore-fail-slow
chore: let all tests run to completion
2022-11-22 19:22:14 +01:00
sofstam
30af26a8b3 Include the mapped reads in samtools stats 2022-11-22 16:50:50 +01:00
James Fellows Yates
a383c9ae40 Remove the join 2022-11-22 13:39:21 +01:00
James Fellows Yates
06659af777 Remove flatten 2022-11-22 13:36:40 +01:00
James Fellows Yates
cacd7d3128 Not just in stub 2022-11-22 13:33:13 +01:00
James Fellows Yates
e8de006ed6 With a join 2022-11-22 13:27:49 +01:00
James Fellows Yates
ebfc84e235 Does the grouping work if we have meta? 2022-11-22 13:26:54 +01:00
James Fellows Yates
21759807f7 Does flatten work? 2022-11-22 12:48:54 +01:00
James Fellows Yates
3102e40052 dump teh db 2022-11-22 12:46:26 +01:00