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836 commits

Author SHA1 Message Date
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
James Fellows Yates
557f2a4d96 Extra dump 2022-11-22 12:26:46 +01:00
James Fellows Yates
5caebcc6ab Append to correct db 2022-11-22 12:21:59 +01:00
James Fellows Yates
52fc00802b Correct meta name for db meta 2022-11-22 12:19:56 +01:00
James Fellows Yates
b8937748d3 Fix meta.id isssue 2022-11-22 12:18:52 +01:00
James Fellows Yates
db334c5185 Fix missing info 2022-11-22 12:17:08 +01:00
James Fellows Yates
0f298dca43 group krakenuniq reads by pairs or single end 2022-11-22 12:13:08 +01:00
Moritz E. Beber
6b538d658a chore: let all tests run to completion 2022-11-22 10:13:10 +01:00
James A. Fellows Yates
10c72f1265
Merge pull request #169 from nf-core/diagram-update
Update tubemap to include samtools stats
2022-11-06 10:15:56 +01:00
James Fellows Yates
f414f5dc9c Add falco to tube map 2022-11-04 18:20:44 +01:00
James Fellows Yates
4275640d9b update tubemap to include samtools stats 2022-11-04 15:24:15 +01:00
James A. Fellows Yates
67e264b7a9
Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools
Add samtools stats for short-reads
2022-11-04 14:39:29 +01:00
Sofia Stamouli
696edfb866 Apply prettier 2022-11-04 12:05:23 +01:00
Sofia Stamouli
d2195e9eda
Merge branch 'dev' into short_reads_samtools 2022-11-04 11:47:36 +01:00
Sofia Stamouli
79dd3930bb
Add samtools to README 2022-11-03 16:52:01 +01:00
James Fellows Yates
461482d22a Try again wit hthe corret param 2022-11-03 15:02:22 +01:00
James Fellows Yates
93f38b14a8 Save report 2022-11-03 15:01:00 +01:00
James Fellows Yates
c5e5696f84 Fix parameter name 2022-11-03 14:58:03 +01:00
James Fellows Yates
c03a21c770 Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module 2022-11-03 14:56:43 +01:00
James Fellows Yates
21a76c2449 Fix cardinality issue 2022-11-03 14:56:26 +01:00
nf-core-bot
0c445759e4 [automated] Fix linting with Prettier 2022-11-03 13:42:39 +00:00
Sofia Stamouli
b5e6639f9d
Apply review suggestions 2022-11-03 14:12:05 +01:00