300 commits

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	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
sofstam	c47b9e55fa	Mix reads in emit	2023-04-04 18:01:02 +02:00
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	8745fc625c	Correct output file from samtools/fastq	2023-03-29 15:36:20 +02:00
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
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	e49668005f	Update docs based on feedback and add missing results directories	2023-03-12 08:35:45 +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
James Fellows Yates	98bc6910d5	Update authors and remove left over comment	2023-03-07 11:47:54 +01:00
James Fellows Yates	6e64c2b5a9	Fix copy paste error	2023-03-06 10:50:36 +01:00
James Fellows Yates	735212c9ee	Fix the non-updated KAIJU2TABLE name	2023-03-06 10:47:36 +01:00
James Fellows Yates	a5138ed6e0	Fix ugly warn when KAIJU2TABLE not run	2023-03-06 08:17:50 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James A. Fellows Yates	32c0d8d6a5	Fix KrakenUniq Taxpasta issue	2023-02-22 08:24:48 +01:00
sofstam	90aa7551a9	Fix the motus_versions	2023-02-20 14:27:57 +01:00
sofstam	3fa1b0c17d	Remove standardised_tables	2023-02-20 13:48:04 +01:00
sofstam	90a5668007	run_malt false in test and add text in output.md	2023-02-17 15:38:36 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
sofstam	2456038567	Merge branch 'dev' into add_taxpasta_merge	2023-02-16 15:07:51 +01:00
sofstam	de6a4214ef	Add taxpasta_merge to taxprofiler	2023-02-16 14:29:52 +01:00
James Fellows Yates	7dfcdd015b	Re-add the 'native' combined kaiju output	2023-02-16 14:02:13 +01:00
James Fellows Yates	79b4db9a34	Move kaiju2table to profiling	2023-02-16 13:39:05 +01:00
James A. Fellows Yates	45ac6fedc2	Merge pull request #237 from nf-core/bracken-params ... Support Kraken and Bracken db_params in database sheet	2023-02-09 10:59:27 +01:00
James A. Fellows Yates	70eb84b8d5	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2023-02-09 08:01:52 +01:00
James Fellows Yates	b3837cce5b	Relax strictness so can supply empty db_params but block if only single parameter with out ;	2023-02-08 15:44:37 +01:00
James Fellows Yates	fe3d42ffd7	Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters	2023-02-08 13:34:36 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +01:00
James Fellows Yates	059cd17114	Fix exporting of mapped/unmapped reads for consistency across both short and long reads	2023-02-07 11:43:40 +01:00
James A. Fellows Yates	47efd193cb	Merge pull request #219 from nf-core/allow-targz-motus [skip ci] ... Allow all tool's databases to be provided as `.tar.gz` files	2023-01-25 13:48:43 +01:00
James A. Fellows Yates	4289e1f901	Remove metaphlan3 nanopore filter as _sometimes_ it can work	2023-01-24 15:42:14 +01:00
James A. Fellows Yates	c765b3f0bc	Merge branch 'dev' into allow-targz-motus	2023-01-24 15:20:29 +01:00
James A. Fellows Yates	00178d3431	Merge pull request #221 from nf-core/metaphlan3-filter-nanopore ... Filter out nanopore data prior Metaphlan3	2023-01-24 14:39:02 +01:00
James Fellows Yates	14826d5205	Separate conditions, remove some left-over dumps	2023-01-24 13:20:58 +01:00