1017 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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	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
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 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	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
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