218 commits

Author	SHA1	Message	Date
James A. Fellows Yates	f7b7fd63a4	Merge pull request #114 from nf-core/nf-core-template-merge-2.5 ... Important! Template update for nf-core/tools v2.5	2022-08-31 10:28:14 +02:00
James A. Fellows Yates	28d8d3f8fb	Merge branch 'dev' into nf-core-template-merge-2.5	2022-08-31 09:16:34 +02:00
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
James Fellows Yates	afba604e8b	Make everything within opt-out, once QC is opted-in	2022-08-30 14:04:34 +02:00
James Fellows Yates	2cc07183a0	Standardise QC parameter system and turn on both porechop/filtlong in tests	2022-08-30 13:58:58 +02:00
James A. Fellows Yates	a3055bf6da	Update conf/test_nothing.config	2022-08-23 15:48:02 +02:00
James Fellows Yates	e6c7939305	Add test_nothing config profile for minimal testing	2022-08-23 14:37:01 +02:00
James Fellows Yates	a97bb69cd2	Prettier	2022-08-23 14:24:57 +02:00
James A. Fellows Yates	de70b0a01d	Merge pull request #109 from nf-core/centrifuge_mqc ... Trying to get Centrifuge output into MQC	2022-07-29 13:36:25 +02:00
mjamy	5cdf5e958a	Updated modules.config to add 'log' in diamond config	2022-07-28 16:08:15 +02:00
sofstam	71cf32cc6a	Add error strategy for centrifuge/kreport	2022-07-28 08:54:32 +02:00
James A. Fellows Yates	65ae82efc4	Define separte krakena nd centrigfue modules	2022-07-26 18:37:33 +00:00
James A. Fellows Yates	e76b299705	Start working getting kraken and centrifuge working in MQC	2022-07-26 08:18:54 +00:00
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James A. Fellows Yates	8082c7d108	Merge pull request #97 from nf-core/malt-to-krona ... Add Krona support for MALT	2022-07-05 15:17:52 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	447b8f0905	Get fixed Krona module and add Krona taxonomy to test profile	2022-07-01 17:21:19 +02:00
James Fellows Yates	02c06b9f7b	Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file	2022-06-30 18:33:11 +02:00
Thomas A. Christensen II	069370db86	Add unclassified and verbose flags to kaiju2krona	2022-06-28 09:00:42 -05:00
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
Thomas A. Christensen II	0e8edd5b2f	Add output configuration for Kraken Krona chart	2022-06-27 08:25:47 -05:00
James Fellows Yates	9462032d00	Fix MALT save_alignemnts reads and some clean up	2022-06-03 22:29:04 +02:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +02:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
James A. Fellows Yates	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James Fellows Yates	d3d28da1b1	Update after review	2022-06-02 11:53:53 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +02:00
JIANHONG OU	f0eb88cbe2	add mOTUs to modules.config	2022-05-31 08:57:00 -04:00
JIANHONG OU	4d77b47e8d	create a new test profile config for mOTUs.	2022-05-31 08:47:38 -04:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James A. Fellows Yates	d67543503b	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-07 13:15:21 +02:00
James Fellows Yates	0f651873dd	Linting	2022-05-07 06:12:24 +02:00
James Fellows Yates	47a5ae0cff	Add FASTP complexity option	2022-05-07 06:09:05 +02:00
James Fellows Yates	87a1d80519	Add working output for Kraken2/Centrifuge/DIAMOND	2022-05-07 05:22:35 +02:00
ljmesi	6618e8cac6	Change param to a more generic name	2022-05-05 13:20:34 +02:00
ljmesi	557d31dfd2	Add parameter for turning on longread host removal	2022-05-05 13:19:10 +02:00
ljmesi	d94534e8ac	Simplify params which control host removal publish	2022-05-05 09:07:33 +02:00
ljmesi	a821f748ee	Add modules	2022-05-03 09:28:46 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	0630fce3b5	Tweak based on official DIAMOND test-data	2022-04-30 08:11:40 +02:00
James Fellows Yates	a4a9b161d8	Lintin	2022-04-29 22:02:44 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
sofstam	d082d67bcb	Add kaiju2table to taxprofiler	2022-04-25 17:36:29 +02:00
Sofia Stamouli	e7e24c2d95	Prettier and suggestions from review	2022-04-25 09:21:29 +02:00
sofstam	c00ca1c2b8	Add centrifuge kreport in taxprofiler	2022-04-22 15:24:10 +02:00
James A. Fellows Yates	63230c3254	Merge pull request #63 from nf-core/maxforks ... Update test.config to only allow maxFork to 1 for MALT_RUN	2022-04-21 12:57:37 +02:00
James A. Fellows Yates	cd3c8f6a89	Merge branch 'dev' into hostremoval-publish-fix	2022-04-21 11:43:06 +02:00
James A. Fellows Yates	d850333e11	Linting	2022-04-20 13:42:26 +02:00
James A. Fellows Yates	d031322c16	Update test.config	2022-04-20 13:41:01 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	d16cd75652	Merge branch 'dev' into hostremoval-publish-fix	2022-04-20 09:53:51 +02:00
sofstam	1b7ff2265d	Update usage.md, reformat test.config and modules.config	2022-04-19 13:04:58 +02:00
James Fellows Yates	9880baa0b8	Get build directory working	2022-04-18 06:37:23 +02:00
James Fellows Yates	2cfcdf2dd2	Add finer controler over for hostremoval saving	2022-04-17 22:27:04 +02:00
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	5e80df0f94	Apply suggestions from code review	2022-04-13 15:27:53 +02:00
James Fellows Yates	aa2d07c42a	Fix merge cockup	2022-04-13 14:19:19 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James Fellows Yates	a5f4fc42d5	Fix run merging for unmerged PE data	2022-04-12 09:25:27 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James Fellows Yates	082093f3de	Prettier	2022-04-10 06:44:10 +02:00
James Fellows Yates	ecf0eea4f9	Move profiling to subworkflow and standardise outputs	2022-04-10 06:43:30 +02:00
James Fellows Yates	ca011ccc5b	Fix cat_fastq naming logic?	2022-04-08 13:28:37 +02:00
James Fellows Yates	d130a72d74	Get this working	2022-04-08 13:09:23 +02:00
Sofia Stamouli	48d28cf8d4	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:10 +02:00
Sofia Stamouli	2dfe3b3cc1	Update conf/test.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-08 10:00:04 +02:00
sofstam	26779a4420	Remove db_name from nextflow.config	2022-04-07 16:27:19 +02:00
sofstam	606e5da7d5	Check if PR works with centrifuge/centrifuge module	2022-04-07 16:13:17 +02:00
James A. Fellows Yates	b554aa3e4d	Merge branch 'dev' into hostremoval	2022-04-07 14:00:10 +02:00
Moritz E. Beber	7ab3aa546b	refactor: use flags to publish reads	2022-04-06 10:27:11 +02:00
Moritz E. Beber	018b9a8ea6	refactor: do not generally publish output	2022-04-06 10:21:43 +02:00
Moritz E. Beber	8827b143a2	fix: disable publishing correctly	2022-04-05 20:56:19 +02:00
Moritz E. Beber	af12435fa5	fix: use parameter for publish mode everywhere	2022-04-05 20:56:19 +02:00
Moritz E. Beber	c40a9a0011	refactor: avoid publishing unpacked databases	2022-04-05 20:54:32 +02:00
James Fellows Yates	d46ddd972c	Expand tests and fix schema after review	2022-04-05 11:04:30 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +02:00
James Fellows Yates	a384162810	Add prinseq as alternative complexity filtering	2022-04-04 21:16:51 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
James A. Fellows Yates	b2e29ea23a	Merge branch 'dev' into hostremoval	2022-04-03 17:24:07 +02:00
James Fellows Yates	066ceb2bca	Remove flagstat as bowtie2 reports this itself	2022-04-03 17:23:14 +02:00
James Fellows Yates	02d950c58c	Fix test so complexity filter actually executes	2022-04-02 17:18:20 +02:00
James Fellows Yates	7f1a7fb4e7	Add complexity filtering to test profile	2022-04-02 17:05:54 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	70862570e0	fix: use same naming scheme	2022-04-02 15:00:26 +02:00
Moritz E. Beber	817678d870	chore: add metaphlan3 run to test profile	2022-04-02 15:00:26 +02:00
Moritz E. Beber	b0b5936fe8	chore: configure output for metaphlan3	2022-04-02 15:00:26 +02:00
James Fellows Yates	dcda815bfb	Add final adapterremoval options to match fastp functionality	2022-04-01 09:50:08 +02:00
James Fellows Yates	76e9624e3f	NOW commit the adapte rtrim flag	2022-03-30 11:31:37 +02:00
James Fellows Yates	98a9688329	Change CPUs back to template, update skiptrim fiag	2022-03-29 15:18:06 +02:00
James Fellows Yates	04fb6f4127	Use new resources for test data	2022-03-28 20:38:16 +02:00
James Fellows Yates	94e5cfef4a	Filter long reads for MALT, bump cpus for FastQC for minigut to pass	2022-03-28 18:20:10 +02:00
James Fellows Yates	231253227c	Remove run merging for now due to complexity	2022-03-28 16:38:10 +02:00
James Fellows Yates	8dc9e583ad	Debugging run merging	2022-03-27 09:30:23 +02:00
James A. Fellows Yates	e6e8ed7cc9	Add some debugging notes	2022-03-26 20:54:50 +00:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James Fellows Yates	ede362dbf9	Remove duplicate config and sync longread fastqc	2022-03-25 15:28:30 +01:00
James Fellows Yates	dfcf8f7b1a	Prettier	2022-03-25 15:10:52 +01:00
James Fellows Yates	ff1f28f4f0	Update schema	2022-03-25 15:01:25 +01:00
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James A. Fellows Yates	038a8d106a	Fix test with correct URL	2022-03-23 11:25:47 +01:00
James Fellows Yates	48b6ef508d	Update path to samplesheet	2022-03-23 10:06:01 +01:00
James Fellows Yates	358b89a4c6	Linting	2022-03-21 20:30:29 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	8012998542	Make parameter naming more consistent for clipmerge	2022-03-21 19:52:50 +01:00
James A. Fellows Yates	631c115e10	Adds PoC of untarring system	2022-03-21 14:58:19 +00:00
ljmesi	16be676d72	Add Porechop module	2022-03-18 14:34:10 +01:00
James A. Fellows Yates	ac77676d2b	Merge branch 'dev' into nf-core-template-merge-2.3	2022-03-17 13:11:34 +01:00
nf-core-bot	699d26b149	Template update for nf-core/tools version 2.3	2022-03-15 21:05:37 +00:00
James Fellows Yates	2c183ed2ed	Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)	2022-03-03 17:42:02 +01:00
James Fellows Yates	cf55cc592c	Get skeleton read processing to input for profiling	2022-02-18 16:51:01 +01:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00