1049 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	2e980f1d15	Update CAT_FASTQ module	2023-05-02 14:03:44 +02:00
James Fellows Yates	87fd5f72d0	Fix template	2023-05-02 13:20:09 +02:00
James Fellows Yates	661cfbe012	Update UNTAR module	2023-05-02 13:20:09 +02:00
James A. Fellows Yates	727291999b	Merge branch 'dev' into nf-core-template-merge-2.8	2023-05-02 13:17:18 +02:00
James A. Fellows Yates	89096beb61	Merge pull request #290 from nf-core/motus-docs-improvements ... Improve mOTUS database input description	2023-04-29 18:36:18 +02:00
James Fellows Yates	f11d7c7bb5	Comment out right part of function	2023-04-29 18:33:12 +02:00
James Fellows Yates	2dc8a88b67	Update changelog	2023-04-29 18:17:09 +02:00
James Fellows Yates	44286bf96d	Improve mOTUS database input desciption	2023-04-29 18:14:30 +02:00
James Fellows Yates	8bc17cccfc	Prettier	2023-04-29 18:09:09 +02:00
James Fellows Yates	1ef8119c59	Linting fixes deactivate accidental re-included function	2023-04-29 18:08:00 +02:00
James A. Fellows Yates	bca6e645a8	Merge branch 'dev' into nf-core-template-merge-2.8	2023-04-29 17:58:15 +02:00
nf-core-bot	ac60d66956	Template update for nf-core/tools version 2.8	2023-04-28 14:26:38 +00:00
James A. Fellows Yates	9850bdf1fa	Merge pull request #287 from nf-core/missing-changelog ... Misssing changelog manual prettier [skip ci]	2023-04-26 08:57:34 +02:00
James A. Fellows Yates	4f08b3697f	Merge branch 'dev' into missing-changelog	2023-04-26 08:57:26 +02:00
Moritz E. Beber	c4ad03ff9f	Merge pull request #276 from nf-core/feat-batch ... feat: introduce sample batches for krakenuniq	2023-04-23 11:17:29 +02:00
Moritz E. Beber	66a166dbdc	docs: tweak parameter schema description	2023-04-22 21:23:27 +02:00
Moritz E. Beber	08f06b9982	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-04-22 21:18:58 +02:00
Moritz E. Beber	49086d9475	docs: add changelog entry ... [skip ci]	2023-04-22 21:15:01 +02:00
Moritz E. Beber	2725fe15a9	docs: create a schema entry for the new parameter	2023-04-22 21:13:19 +02:00
Moritz E. Beber	17a9493e6d	fix: remove typo	2023-04-22 21:13:19 +02:00
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 Fellows Yates	e000ac3038	Misssing changelog manual prettier [skip ci]	2023-04-21 06:09:49 +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