sofstam
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30af26a8b3
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Include the mapped reads in samtools stats
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2022-11-22 16:50:50 +01:00 |
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James Fellows Yates
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a383c9ae40
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Remove the join
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2022-11-22 13:39:21 +01:00 |
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James Fellows Yates
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06659af777
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Remove flatten
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2022-11-22 13:36:40 +01:00 |
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James Fellows Yates
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cacd7d3128
|
Not just in stub
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2022-11-22 13:33:13 +01:00 |
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James Fellows Yates
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e8de006ed6
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With a join
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2022-11-22 13:27:49 +01:00 |
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James Fellows Yates
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ebfc84e235
|
Does the grouping work if we have meta?
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2022-11-22 13:26:54 +01:00 |
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James Fellows Yates
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21759807f7
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Does flatten work?
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2022-11-22 12:48:54 +01:00 |
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James Fellows Yates
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3102e40052
|
dump teh db
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2022-11-22 12:46:26 +01:00 |
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James Fellows Yates
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557f2a4d96
|
Extra dump
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2022-11-22 12:26:46 +01:00 |
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James Fellows Yates
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5caebcc6ab
|
Append to correct db
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2022-11-22 12:21:59 +01:00 |
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James Fellows Yates
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52fc00802b
|
Correct meta name for db meta
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2022-11-22 12:19:56 +01:00 |
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James Fellows Yates
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b8937748d3
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Fix meta.id isssue
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2022-11-22 12:18:52 +01:00 |
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James Fellows Yates
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db334c5185
|
Fix missing info
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2022-11-22 12:17:08 +01:00 |
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James Fellows Yates
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0f298dca43
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group krakenuniq reads by pairs or single end
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2022-11-22 12:13:08 +01:00 |
|
Moritz E. Beber
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6b538d658a
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chore: let all tests run to completion
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2022-11-22 10:13:10 +01:00 |
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James A. Fellows Yates
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10c72f1265
|
Merge pull request #169 from nf-core/diagram-update
Update tubemap to include samtools stats
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2022-11-06 10:15:56 +01:00 |
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James Fellows Yates
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f414f5dc9c
|
Add falco to tube map
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2022-11-04 18:20:44 +01:00 |
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James Fellows Yates
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4275640d9b
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update tubemap to include samtools stats
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2022-11-04 15:24:15 +01:00 |
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James A. Fellows Yates
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67e264b7a9
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Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools
Add samtools stats for short-reads
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2022-11-04 14:39:29 +01:00 |
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Sofia Stamouli
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696edfb866
|
Apply prettier
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2022-11-04 12:05:23 +01:00 |
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Sofia Stamouli
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d2195e9eda
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Merge branch 'dev' into short_reads_samtools
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2022-11-04 11:47:36 +01:00 |
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Sofia Stamouli
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79dd3930bb
|
Add samtools to README
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2022-11-03 16:52:01 +01:00 |
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James Fellows Yates
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461482d22a
|
Try again wit hthe corret param
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2022-11-03 15:02:22 +01:00 |
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James Fellows Yates
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93f38b14a8
|
Save report
|
2022-11-03 15:01:00 +01:00 |
|
James Fellows Yates
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c5e5696f84
|
Fix parameter name
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2022-11-03 14:58:03 +01:00 |
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James Fellows Yates
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c03a21c770
|
Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module
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2022-11-03 14:56:43 +01:00 |
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James Fellows Yates
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21a76c2449
|
Fix cardinality issue
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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 |
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James A. Fellows Yates
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bc671c547d
|
Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
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2022-11-03 14:08:13 +01:00 |
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James Fellows Yates
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6459d8920f
|
Linting!
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2022-11-03 14:05:43 +01:00 |
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James A. Fellows Yates
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1f31f88635
|
Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
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2022-11-03 11:36:14 +01:00 |
|
James A. Fellows Yates
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62f45c8be7
|
Update nextflow.config
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2022-11-03 10:03:27 +01:00 |
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James A. Fellows Yates
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24dc2a2cec
|
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-11-03 10:03:07 +01:00 |
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James Fellows Yates
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d487a1ff2f
|
Addd FASTP adadapter list
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2022-11-02 12:39:34 +01:00 |
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Sofia Stamouli
|
e4307ad8ab
|
Change modules.config to include porechop_porechop
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2022-11-01 20:50:42 +01:00 |
|
Sofia Stamouli
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3faea8aac5
|
Fix porechop conflict
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2022-11-01 17:34:37 +01:00 |
|
Mahwash Jamy
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aecf308840
|
Update documentation for krakenuniq
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2022-10-31 16:41:35 +00:00 |
|
Mahwash Jamy
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851016e497
|
Update nextflow_scheme.json
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2022-10-31 16:17:40 +00:00 |
|
Mahwash Jamy
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febcbfc057
|
add missing parameters to nextflow.config
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2022-10-31 16:07:53 +00:00 |
|
Mahwash Jamy
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3147a80a56
|
Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module
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2022-10-31 15:36:57 +00:00 |
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Sofia Stamouli
|
0e0c55d3b0
|
Update modules.config
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2022-10-31 12:35:51 +01:00 |
|
Sofia Stamouli
|
a4b5fa9f57
|
Fix trailing space
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2022-10-31 12:17:49 +01:00 |
|
Sofia Stamouli
|
1d1047374b
|
Fix EditorConfig format
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2022-10-31 12:09:25 +01:00 |
|
Sofia Stamouli
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074d3ec204
|
Merge pull request #161 from genomic-medicine-sweden/samtools_stats
Add samtools stats for long-reads
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2022-10-31 10:59:37 +01:00 |
|
Sofia Stamouli
|
ce611d6efd
|
Add bowtie2 mapped reads
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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 |
|