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660 commits

Author SHA1 Message Date
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
James A. Fellows Yates
bc671c547d
Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
2022-11-03 14:08:13 +01:00
James Fellows Yates
6459d8920f Linting! 2022-11-03 14:05:43 +01:00
James A. Fellows Yates
1f31f88635
Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
2022-11-03 11:36:14 +01:00
James A. Fellows Yates
62f45c8be7
Update nextflow.config 2022-11-03 10:03:27 +01:00
James A. Fellows Yates
24dc2a2cec
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-11-03 10:03:07 +01:00
James Fellows Yates
d487a1ff2f Addd FASTP adadapter list 2022-11-02 12:39:34 +01:00
Sofia Stamouli
e4307ad8ab Change modules.config to include porechop_porechop 2022-11-01 20:50:42 +01:00
Sofia Stamouli
3faea8aac5 Fix porechop conflict 2022-11-01 17:34:37 +01:00
Mahwash Jamy
aecf308840 Update documentation for krakenuniq 2022-10-31 16:41:35 +00:00
Mahwash Jamy
851016e497 Update nextflow_scheme.json 2022-10-31 16:17:40 +00:00
Mahwash Jamy
febcbfc057 add missing parameters to nextflow.config 2022-10-31 16:07:53 +00:00
Mahwash Jamy
3147a80a56 Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module 2022-10-31 15:36:57 +00:00
Sofia Stamouli
0e0c55d3b0
Update modules.config 2022-10-31 12:35:51 +01:00
Sofia Stamouli
a4b5fa9f57
Fix trailing space 2022-10-31 12:17:49 +01:00
Sofia Stamouli
1d1047374b
Fix EditorConfig format 2022-10-31 12:09:25 +01:00
Sofia Stamouli
074d3ec204
Merge pull request #161 from genomic-medicine-sweden/samtools_stats
Add samtools stats for long-reads
2022-10-31 10:59:37 +01:00
Sofia Stamouli
ce611d6efd Add bowtie2 mapped reads 2022-10-31 10:04:51 +01:00
Sofia Stamouli
f1778acf35
Apply review suggestion 2022-10-31 09:31:13 +01:00
Sofia Stamouli
c4a7d094c8 Fix EditorConfig check 2022-10-28 14:33:44 +02:00
Sofia Stamouli
5b99d9024a Add samtools stats for short-reads 2022-10-28 14:24:33 +02:00
Sofia Stamouli
f87131c7b1 Save samtools stats output 2022-10-28 14:10:24 +02:00