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997 commits

Author SHA1 Message Date
nf-core-bot
4f7e2eed8c [automated] Fix linting with Prettier 2023-04-20 13:11:19 +00:00
James A. Fellows Yates
b3e602dcb3
Merge branch 'dev' into replace-exit-with-error 2023-04-20 14:38:25 +02:00
Sofia Stamouli
255b492b44
Merge pull request #274 from sofstam/samtools_fastq
Subsitute samtools/bam2fq with samtools/fastq
2023-04-18 16:28:31 +02:00
sofstam
c47b9e55fa Mix reads in emit 2023-04-04 18:01:02 +02:00
James A. Fellows Yates
59f8d75e9e update CHAGENLGO 2023-04-04 09:43:01 +00:00
James A. Fellows Yates
03c3169f10 Replace all instance of exit 1 with error for safety and consistency 2023-04-04 09:41:22 +00:00
sofstam
d6b60643d9 Prettier 2023-03-31 10:35:40 +02:00
sofstam
021f5f0a22 Remove samtools/bam2fq module 2023-03-31 10:28:36 +02:00
sofstam
8745fc625c Correct output file from samtools/fastq 2023-03-29 15:36:20 +02:00
sofstam
e274823f73 Add conf for samtools/fastq 2023-03-27 12:42:28 +02:00
sofstam
a3d077fcbc Prettier 2023-03-23 17:05:34 +01:00
sofstam
85905127b8 Update changelog 2023-03-23 15:34:47 +01:00
sofstam
102d53bd75 Subsitute samtools/bam2fq with samtools/fastq 2023-03-23 15:30:07 +01:00
Sofia Stamouli
58795264e4
Merge pull request #271 from nf-core/prototaxites-docs-updates
Standardised taxon table and mOTU database docs improvement
2023-03-21 10:14:14 +01:00
Sofia Stamouli
e0b112cdce
Merge branch 'dev' into prototaxites-docs-updates 2023-03-21 08:44:48 +01:00
James A. Fellows Yates
8deb32da72
Merge pull request #270 from nf-core/index-warn-fix
Fix broken check for host read removal index
2023-03-20 21:10:40 +01:00
James Fellows Yates
b0939c3ae9 Standardised taxon table and mOTU database docs improvement 2023-03-17 21:03:54 +01:00
James Fellows Yates
fbecfb6f33 Fix broken check for host read removal index 2023-03-17 20:47:09 +01:00
James A. Fellows Yates
af61e007b3
Merge pull request #269 from nf-core/reduce-full-test-output
Deactivate saving of reads and other large files for full tests
2023-03-17 11:46:08 +01:00
James A. Fellows Yates
142ff2f099
Apply suggestions from code review 2023-03-17 10:26:38 +01:00
James Fellows Yates
577d270423 Deactivate saving of reads and other large files for full tests 2023-03-17 10:14:40 +01:00
James A. Fellows Yates
66a98c2bc8
Merge pull request #265 from genomic-medicine-sweden/dev
Update changelog after release
2023-03-13 12:56:40 +01:00
sofstam
1347f27c11 Update changelog after release 2023-03-13 12:21:37 +01:00
James A. Fellows Yates
eaef6ac9bc
Apply suggestions from code review 2023-03-13 10:57:36 +01:00
Sofia Stamouli
ae3ee470ee
Merge pull request #264 from sofstam/update_taxpasta_version
Updata taxpasta 0.2.3
2023-03-13 10:25:55 +01:00
Sofia Stamouli
0007c99d1c
Merge branch 'dev' into update_taxpasta_version 2023-03-13 09:38:10 +01:00
sofstam
8ecb655952 Prettier 2023-03-13 09:11:53 +01:00
sofstam
213f4e4f23 Updata taxpasta 2023-03-13 08:58:59 +01:00
James A. Fellows Yates
3c4ee927e3
Merge pull request #263 from nf-core/docs-updates
Update docs based on feedback and add missing results directories
2023-03-12 12:10:34 +01:00
James A. Fellows Yates
9550c76c25
Update README.md 2023-03-12 11:11:05 +01:00
James A. Fellows Yates
7f6e162e1c
Update docs/output.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-03-12 11:08:37 +01:00
James A. Fellows Yates
6266ee782d
Update README.md
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
2023-03-12 11:08:31 +01:00
James Fellows Yates
95f9bf1fa9 Update credits section 2023-03-12 08:43:56 +01:00
James Fellows Yates
e49668005f Update docs based on feedback and add missing results directories 2023-03-12 08:35:45 +01:00
Moritz E. Beber
efa398edab
Merge pull request #258 from nf-core/clone-maps
refactor: double check maps and validation
2023-03-11 21:39:49 +01:00
James A. Fellows Yates
5e400c8c89
Apply suggestions from code review 2023-03-11 20:06:59 +01:00
Moritz E. Beber
bb7323e25d fix: restore setting id on FASTQ meta 2023-03-11 11:34:47 +01:00
Moritz E. Beber
7104b12e3b Update subworkflows/local/longread_preprocessing.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2023-03-11 11:28:42 +01:00
Moritz E. Beber
fa1c779536 fix: insert id key again 2023-03-11 11:28:42 +01:00
Moritz E. Beber
246da8a7b0 chore: remove fixme comments 2023-03-11 11:28:42 +01:00
Moritz E. Beber
7c1133efb8 add more comments and slight style changes 2023-03-11 11:28:42 +01:00
Moritz E. Beber
5380bc18ec fix: channels should match 1:1 without remaining elements 2023-03-11 11:28:42 +01:00
Moritz E. Beber
07db3c93e2 style: use map addition instead of cloning 2023-03-11 11:28:42 +01:00
Moritz E. Beber
d17dce5590 style: use subMap and early returns 2023-03-11 11:28:42 +01:00
Moritz E. Beber
0bcea6c993 style: use parameter for branch closure 2023-03-11 11:28:42 +01:00
Moritz E. Beber
b90433f3c2 style: use parameters for filter closure 2023-03-11 11:28:42 +01:00
Moritz E. Beber
aa2410a871 style: use named parameters for closure 2023-03-11 11:28:42 +01:00
Moritz E. Beber
c2ad421051 refactor: simplify DB validation 2023-03-11 11:28:42 +01:00
Sofia Stamouli
53db964bcf
Merge pull request #260 from alexhbnr/spelling_mistake_README
Update README.md
2023-03-10 14:03:58 +01:00
Alex Hübner
f92a405554
Update README.md 2023-03-10 12:36:52 +01:00