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Author	SHA1	Message	Date
Thomas A. Christensen II	a84f693479	Install KRAKENTOOLS_KREPORT2KRONA module	2022-06-14 08:13:36 -05:00
James A. Fellows Yates	3dcda7446b	Merge pull request #86 from nf-core/support-aligned-reads ... Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND	2022-06-13 11:23:34 +02:00
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 Fellows Yates	6c6f5e0913	Merge branch 'dev' of github.com:nf-core/taxprofiler into dev	2022-06-09 08:21:51 +02:00
James Fellows Yates	ec13b8d608	Remove support for uncompressed FASTQ files	2022-06-09 08:21:48 +02:00
James Fellows Yates	800c0dd2aa	Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads	2022-06-09 08:16:01 +02:00
James Fellows Yates	490a8a8a84	Remove dump	2022-06-09 08:15:58 +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
James Fellows Yates	d48b3be5a7	Tweak DIAMOND save_reads message	2022-06-03 13:55:17 +02:00
James Fellows Yates	3313b90453	Fix JSOn schema	2022-06-03 13:50:48 +02:00
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +02:00
James A. Fellows Yates	43ea8d299c	Merge pull request #74 from nf-core/add-filtlong ... Add initial longread QC filtering - requires filtlong module update	2022-06-02 20:10:46 +02:00
James Fellows Yates	2838c136bd	Prettier	2022-06-02 12:51:39 +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 A. Fellows Yates	a196e0f628	Merge branch 'dev' into add-filtlong	2022-06-02 11:51:26 +02:00
James A. Fellows Yates	dfcaaae1fb	Merge pull request #83 from ZandraFagernas/dev ... Uploaded logo	2022-06-02 11:31:32 +02:00
James Fellows Yates	fa70a413cb	Use finally working filtlong module	2022-05-31 21:12:09 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +02:00
James Fellows Yates	792e2d019b	Fix merge error in schema	2022-05-31 13:06:48 +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
James Fellows Yates	77da358e87	Separate dark and light mode logos, add to README and add to MQC report	2022-05-31 12:45:38 +02:00
ZandraFagernas	74b48f0919	Add files via upload	2022-05-28 13:29:24 +02:00
James A. Fellows Yates	ba75685550	Merge pull request #81 from nf-core/nf-core-template-merge-2.4 ... Important! Template update for nf-core/tools v2.4	2022-05-19 11:00:48 +01:00
Moritz E. Beber	a9fbe47992	Merge branch 'dev' into nf-core-template-merge-2.4	2022-05-19 08:42:28 +02:00
nf-core-bot	a560492353	Template update for nf-core/tools version 2.4	2022-05-16 10:22:38 +00:00
James A. Fellows Yates	63d9cbbdfd	Merge pull request #80 from nf-core/activate-pipeline-specific-profiles ... Activate institutional specific profiles	2022-05-12 11:00:49 +02:00
James A. Fellows Yates	aca7bc439d	Update nextflow.config	2022-05-12 08:08:14 +01:00
James A. Fellows Yates	fd71b71929	Merge pull request #79 from nf-core/fastp-complexity ... Add FASTP complexity option	2022-05-07 14:05:32 +02:00
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	3fa2181f49	Fix prinseq tool selection	2022-05-07 06:15:15 +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
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
Lauri Mesilaakso	e52a40cc9d	Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2 ... Add nanopore host reads removal with minimap2	2022-05-06 12:29:17 +03:00
Lauri Mesilaakso	02517733aa	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 10:40:59 +02:00
Lauri Mesilaakso	b0faeedc60	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 08:20:31 +02:00
ljmesi	e3e55f57c2	Fix alignment ... Just made this change to see if the CI tests would fail again or if the failure was just a one of thing.	2022-05-05 14:02:24 +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	5b7b214156	Fix formatting with prettier	2022-05-05 08:40:53 +02:00
ljmesi	59c7f5a5b1	Update samtools/bam2fq	2022-05-05 08:38:41 +02:00
ljmesi	f4abbe280a	Fix back to nf-core modules version	2022-05-03 12:56:49 +02:00
ljmesi	c833d4fd9a	Fix issues found with prettier	2022-05-03 11:42:05 +02:00
ljmesi	58d4dec70b	Update samtools view	2022-05-03 11:09:54 +02:00
ljmesi	17039ebc6b	Fix type to boolean for flags	2022-05-03 11:07:23 +02:00