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605 commits

Author SHA1 Message Date
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +01:00
nf-core-bot
8067012c01 [automated] Fix linting with Prettier 2022-12-01 09:15:35 +00:00
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
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
James Fellows Yates
d6c0ebb4c6 Prettier 2022-11-29 10:14:33 +01:00
James Fellows Yates
f13185d98b Fix schema location ofr fastqc/falco option 2022-11-29 10:13:46 +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
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
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 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
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
Sofia Stamouli
1bd6dbfe58 Add samtools stats for long-reads 2022-10-28 11:40:50 +02:00
Moritz E. Beber
bf89525bc2
Merge pull request #146 from nf-core/feat-bracken
add Bracken to the profiling workflow
2022-10-27 17:35:06 +02:00