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Author SHA1 Message Date
Moritz E. Beber
70dd7cade9 feat: introduce sample batches for krakenuniq 2023-04-22 21:13:19 +02:00
James A. Fellows Yates
b299a25bc7
Merge pull request #286 from nf-core/multiqc-optimisations 
MultiQC Optimisations
 2023-04-21 22:44:36 +02:00
James A. Fellows Yates
9fa458f381
Merge pull request #279 from nf-core/manifest-update 
Reduce authors to main + other contributors
 2023-04-21 22:44:11 +02:00
James A. Fellows Yates
2140928638
Merge pull request #272 from nf-core/final-reads-saving 
Add 'final reads for profiling' saving mechanism
 2023-04-21 15:21:35 +02:00
James A. Fellows Yates
ee76a5f38b
Update conf/modules.config 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-04-21 13:44:03 +02:00
James A. Fellows Yates
5a09319fb3
Merge branch 'dev' into multiqc-optimisations 2023-04-21 05:58:23 +02:00
James A. Fellows Yates
003862d9ea
Merge pull request #285 from nf-core/update-kraken 
BUmp Kraken2 nf-core module to prevent huge logs
 2023-04-21 05:57:27 +02:00
James A. Fellows Yates
c3c91780ab
Merge pull request #280 from nf-core/replace-exit-with-error 
Replace all instance of exit 1 with error for safety and consistency
 2023-04-21 05:56:44 +02:00
nf-core-bot
386b1c9dfd [automated] Fix linting with Prettier 2023-04-21 03:56:12 +00:00
James A. Fellows Yates
d06ac3713d
Update README.md 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-04-21 05:55:14 +02:00
James Fellows Yates
59f31469c3 Update CHANGELOG 2023-04-20 16:01:22 +02:00
James Fellows Yates
1eb951715f MultiQC optimisations for DIAMOND and Falco 2023-04-20 15:57:57 +02:00
James Fellows Yates
0ed110c529 BUmp Kraken2 nf-core module to prevent huge logs 2023-04-20 15:20:26 +02:00
nf-core-bot
4f7e2eed8c [automated] Fix linting with Prettier 2023-04-20 13:11:19 +00:00
James Fellows Yates
31e3c21dcb Make all saveAs conditions consistent 2023-04-20 15:10:39 +02:00
James A. Fellows Yates
f476b49d29
Add team sectionb 2023-04-20 15:05:49 +02:00
James Fellows Yates
5d90c775e9 Logic safety! 2023-04-20 14:59:07 +02:00
James A. Fellows Yates
b3e602dcb3
Merge branch 'dev' into replace-exit-with-error 2023-04-20 14:38:25 +02:00
James A. Fellows Yates
0245c4880b
Merge branch 'dev' into final-reads-saving 2023-04-20 14:18:10 +02:00
James A. Fellows Yates
105bac7bb9
Apply suggestions from code review 2023-04-20 12:59:33 +02:00
James A. Fellows Yates
ee031ebf91
Apply suggestions from code review 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-04-20 12:58:23 +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
James Fellows Yates
3f34603c00 Prettier 2023-04-15 12:54:07 +02:00
James Fellows Yates
ce97a1124e Add final documentation 2023-04-15 12:48:52 +02:00
James Fellows Yates
94e88d788d Everywhere account when no-runmerging for single libs 2023-04-04 18:36:37 +02:00
sofstam
c47b9e55fa Mix reads in emit 2023-04-04 18:01:02 +02:00
James Fellows Yates
e5e0aab59d More tweaks 2023-04-04 16:29:37 +02:00
James Fellows Yates
ca9c0cf8fd Further fixes 2023-04-04 15:52:23 +02:00
James A. Fellows Yates
5eee462b5a
Update LICENSE 2023-04-04 11:45:06 +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
James A. Fellows Yates
1eeeb8a214
Reduce authors to main + other contributors 
Due to tower limitation producing ugly warning
 2023-04-04 11:19:22 +02:00
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
James Fellows Yates
6895e45768 Fix a few conditional bugs and related 2023-03-23 15:46:02 +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
James Fellows Yates
3b90064ba4 Start adding conditions in modules.conf - non-cat not working 2023-03-22 15:39:45 +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
74bc6b7dd3 Logical ordering and improved commenting 2023-03-17 22:38:05 +01:00
James Fellows Yates
68d131af34 Remove leftover dump 2023-03-17 22:30:43 +01:00
James Fellows Yates
f9af0040bf Add multi-run meta information 2023-03-17 22:30:29 +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