190 commits

Author	SHA1	Message	Date
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
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
sofstam	5a2fd260fd	Log file into multiqc channel	2022-07-15 12:50:50 +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
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
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	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
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	4de43040a3	Switch to using raw classifications for Kaiju2Krona	2022-06-28 09:00:41 -05:00
Thomas A. Christensen II	821dd844d8	Add Kaiju profile conversion to visualization workflow	2022-06-27 09:23:20 -05:00
Thomas A. Christensen II	23fec89b06	Add Krona chart creation for Centrifuge reports	2022-06-27 08:52:29 -05:00
Thomas A. Christensen II	a40a442178	Create VISUALIZATION_KRONA workflow to create Krona charts	2022-06-27 08:22:47 -05:00
James Fellows Yates	e0ad49ebc9	Fix metadata manipulaton for malt	2022-06-10 19:33:37 +02:00
James A. Fellows Yates	621b6a3d09	Add comments about MALT id replacement and refactor for simplicity	2022-06-10 11:27:51 +02:00
James A. Fellows Yates	ebdd5683b2	Apply suggestions from code review	2022-06-03 22:33:48 +02:00
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	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
JIANHONG OU	4b3216c1cb	filter fasta inputs for mOTUs; ... fix the typo for nopreprocessing in nextflow.config.	2022-05-24 08:42:18 -04:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
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
James A. Fellows Yates	e7b54801ed	Merge pull request #75 from nf-core/improve-error-message ... Only create profiler input channels when profiler activated	2022-05-06 11:51:33 +02:00
ljmesi	5e6be52fab	Implement hostremoval	2022-05-03 09:34:27 +02:00
James Fellows Yates	d5049a34e4	Add missing close bracket	2022-05-01 07:28:29 +02:00
James Fellows Yates	4094706421	Only create profiler input channels when profiler activate	2022-05-01 07:24:58 +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	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
James A. Fellows Yates	bc84afe80d	Merge pull request #66 from nf-core/versions-fix ... Fix version reporting	2022-04-25 16:38:28 +02:00
James Fellows Yates	06b38f3699	Fix crash, add missing versions	2022-04-23 08:36:01 +02:00
sofstam	c00ca1c2b8	Add centrifuge kreport in taxprofiler	2022-04-22 15:24:10 +02:00
Sofia Stamouli	e71e7b86a2	Merge pull request #53 from genomic-medicine-sweden/classification_kaiju ... Add kaiju/kaiju in taxprofiler	2022-04-20 10:57:00 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	571495c812	Merge pull request #60 from nf-core/fasta-filtering ... Adds filtering out of FASTA for tools that don't support it	2022-04-20 10:11:17 +02:00
James Fellows Yates	9fd94b1389	Switch to string interpolation	2022-04-20 09:25:54 +02:00
James Fellows Yates	60d232d62c	Revert "Update subworkflows/local/profiling.nf" ... This reverts commit b7d0557ee0.	2022-04-20 09:23:38 +02:00
James A. Fellows Yates	b7d0557ee0	Update subworkflows/local/profiling.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-20 09:15:45 +02:00
James A. Fellows Yates	87777a4289	Update subworkflows/local/profiling.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-19 12:54:57 +02:00
James A. Fellows Yates	ecaff371aa	Update input_check.nf	2022-04-18 07:35:19 +02:00
James A. Fellows Yates	9f634805e4	Update subworkflows/local/profiling.nf	2022-04-18 07:31:44 +02:00
James A. Fellows Yates	9c3c8f1f4e	Merge branch 'dev' into fasta-filtering	2022-04-18 07:31:14 +02:00
James Fellows Yates	6307a9cf43	Typos	2022-04-18 07:28:09 +02:00
James Fellows Yates	491c2d8949	Revert "Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages." ... This reverts commit 564474cafe.	2022-04-18 07:26:15 +02:00
James Fellows Yates	564474cafe	Adds filtering and warning for non-FASTA supporting tool. Standardised warning messages.	2022-04-18 07:21:12 +02:00
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00
James A. Fellows Yates	6fecb3eeb7	Merge pull request #54 from nf-core/dev ... Get upstream changes	2022-04-16 06:17:33 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	de57340526	Start work	2022-04-13 11:49:35 +02:00
James Fellows Yates	a15c45b00c	Put map in the rigt place	2022-04-12 10:51:27 +02:00
James Fellows Yates	8d68914192	Re-add operator name	2022-04-12 10:47:44 +02:00
James Fellows Yates	26399718b2	Re-add pairment attachment	2022-04-12 10:46:03 +02:00
James Fellows Yates	2ef21c6ef3	Fix input to profiling	2022-04-12 10:14:05 +02:00
James Fellows Yates	9f221f84cc	Only supply single input channel to profiling, as these are merged into single input channel at run_merging	2022-04-12 10:12:17 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James Fellows Yates	030099c559	A bit of clean up	2022-04-10 07:26:20 +02:00
James Fellows Yates	ecf0eea4f9	Move profiling to subworkflow and standardise outputs	2022-04-10 06:43:30 +02:00
James Fellows Yates	35cb6e042a	Flatten the right thing	2022-04-08 13:46:12 +02:00
James Fellows Yates	6c14f2b230	Remove the flattening?	2022-04-08 13:44:52 +02:00
James Fellows Yates	a634814d84	Formatting and fix fastp output	2022-04-08 13:34:00 +02:00
James Fellows Yates	d130a72d74	Get this working	2022-04-08 13:09:23 +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
James Fellows Yates	82aa89ad63	re add missing switch meta of merged reads to true	2022-04-05 13:55:11 +02:00
James Fellows Yates	98f082d7b6	Fix mistake in previous upstream merge with AR2 output channel for settings file	2022-04-05 13:17:54 +02:00
James A. Fellows Yates	23fb319779	Merge branch 'dev' into complexity-filter-bbduk	2022-04-05 13:11:15 +02:00
James Fellows Yates	245a4d1f5d	Fix MQC staging and remove debugging dump	2022-04-05 13:08:44 +02:00
Moritz E. Beber	39e5e802c7	refactor: make code more explicit, add comment	2022-04-05 11:29:39 +02:00
Moritz E. Beber	0e9b2989e3	refactor: remove superfluous ENSURE_FASTQ_EXTENSION	2022-04-05 10:53:04 +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	482112bb42	Start work on host removal	2022-04-03 07:58:40 +02:00