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Author	SHA1	Message	Date
James A. Fellows Yates	65ae82efc4	Define separte krakena nd centrigfue modules	2022-07-26 18:37:33 +00:00
James A. Fellows Yates	9d2be68fb8	Merge branch 'dev' into centrifuge_mqc	2022-07-26 18:01:30 +00:00
James A. Fellows Yates	1ef0975736	Merge branch 'dev' into porechop-log	2022-07-26 18:00:28 +00:00
James A. Fellows Yates	fdd9a3bc4d	Merge pull request #107 from nf-core/fix-multiqc-mixing ... Fix MultiQC mixing	2022-07-26 12:38:52 +02:00
James A. Fellows Yates	65b0af9a8b	Fix profiling channels	2022-07-26 08:53:43 +00:00
James A. Fellows Yates	3054dea7c2	Get multiqc input working	2022-07-26 08:41:06 +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	139cf0d6aa	Fix	2022-07-26 10:12:33 +02:00
James A. Fellows Yates	64f01fcfe0	Merge branch 'dev' into porechop-log	2022-07-20 14:05:23 +02:00
Sofia Stamouli	1fe9c133f1	Merge pull request #103 from genomic-medicine-sweden/update_filtlong ... Update the dev branch with the filtlong update	2022-07-20 10:44:52 +02:00
James Fellows Yates	255afee4c7	Re-add the collects	2022-07-19 17:10:10 +02:00
Mahwash Jamy	811ded38af	Update subworkflows/local/profiling.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-07-19 16:44:48 +02:00
Sofia Stamouli	237e9aa623	Update longread_preprocessing.nf	2022-07-19 16:44:08 +02:00
James A. Fellows Yates	8d7ddb5847	Apply suggestions from code review	2022-07-19 16:30:13 +02:00
mjamy	c4c82212e1	incorporate diamond log file into multiqc channel	2022-07-19 14:12:16 +02:00
sofstam	171258d545	Fix typos	2022-07-19 14:07:13 +02:00
sofstam	25bc01f9c4	Fix typos	2022-07-19 14:04:49 +02:00
sofstam	8147dba0b4	Fix typos	2022-07-19 14:03:10 +02:00
sofstam	526ed79763	Fix filtlong logs	2022-07-19 14:01:11 +02:00
sofstam	1ba6a08135	Seperate multiqc for filtlong	2022-07-19 13:53:29 +02:00
James Fellows Yates	33a5402b25	Add emitting porechop logs to multiqc and fix collection of others	2022-07-19 13:50:39 +02:00
sofstam	3f5fa8cc7a	Merge branch 'dev' into update_filtlong	2022-07-19 13:50:28 +02:00
James A. Fellows Yates	6f269a8245	Merge pull request #101 from nf-core/motus/merge ... Add motus/merge and biom support	2022-07-19 13:41:51 +02:00
mjamy	035b4b7a17	Update the dev branch with the DIAMOND module update	2022-07-15 16:28:07 +02:00
sofstam	5a2fd260fd	Log file into multiqc channel	2022-07-15 12:50:50 +02:00
James Fellows Yates	d83c747533	Fix modules JSON	2022-07-15 12:38:20 +02:00
James A. Fellows Yates	c215ed5607	Merge branch 'dev' into motus/merge	2022-07-15 10:52:42 +02:00
James A. Fellows Yates	cc3967a3fd	Apply suggestions from code review	2022-07-15 10:51:41 +02:00
sofstam	6b00360ff5	Merge branch 'dev' into update_filtlong	2022-07-15 10:05:43 +02:00
James A. Fellows Yates	d7ca3df160	Merge pull request #104 from nf-core/motus-profile-update ... Update mOTUs profile module and mix log for multiqc	2022-07-14 16:03:01 +02:00
James Fellows Yates	449b6a5553	Fix file name output clashing wiht multiqc	2022-07-13 15:25:58 +02:00
James Fellows Yates	31119f83c2	Send to MQC only the log file not the meta	2022-07-13 14:29:47 +02:00
James Fellows Yates	13280e2468	Fix .empty	2022-07-13 12:44:44 +02:00
James Fellows Yates	eaa69b65d8	Update mOTUs profile module and mix log for multiqc	2022-07-13 12:38:30 +02:00
James Fellows Yates	c22946cfab	Fix motu versions not being exported if not run	2022-07-13 12:36:29 +02:00
sofstam	1fbe241d27	Update filtlong module	2022-07-12 17:43:52 +02:00
sofstam	4a316df209	Update the dev branch with the filtlong update	2022-07-12 17:15:36 +02:00
James Fellows Yates	d8c0e9e7fe	Prettier	2022-07-12 11:41:07 +02:00
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	1eba859bf8	Merge pull request #82 from jianhong/motus ... add motus profile.	2022-07-04 14:16:12 +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	97e6cdf4b4	Add Krona taxonomy DB to schema build	2022-06-30 18:36:13 +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
James Fellows Yates	27f174d17e	Merge remote-tracking branch 'origin/dev' into malt-to-krona	2022-06-30 12:01:33 +02:00
James Fellows Yates	0050f45345	Add taxonomy directory param	2022-06-30 11:43:52 +02:00
James A. Fellows Yates	913080a5b1	Merge pull request #96 from MillironX/feature/kaiju2krona ... Add Krona output for Kaiju profiles	2022-06-29 09:27:25 +02:00
Thomas A. Christensen II	6673ccf8d8	Update channel assignment alignment in profiling subworkflow ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-06-28 09:00:43 -05:00
Thomas A. Christensen II	069370db86	Add unclassified and verbose flags to kaiju2krona	2022-06-28 09:00:42 -05:00