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Author	SHA1	Message	Date
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
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