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Author	SHA1	Message	Date
James A. Fellows Yates	fb5347a9fc	Merge pull request #58 from nf-core/docs ... Add documentation for preprocessing subworkflows	2022-04-20 09:26:53 +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	ac714dd30f	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-20 09:22:10 +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
Sofia Stamouli	4e1b1269be	Apply prettier	2022-04-19 13:11:43 +02:00
Sofia Stamouli	dc276e8bae	Merge branch 'nf-core:dev' into classification_kaiju	2022-04-19 13:09:15 +02:00
sofstam	1b7ff2265d	Update usage.md, reformat test.config and modules.config	2022-04-19 13:04:58 +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	9880baa0b8	Get build directory working	2022-04-18 06:37:23 +02:00
James Fellows Yates	b036ed5b73	Prettier	2022-04-17 22:28:18 +02:00
James Fellows Yates	2cfcdf2dd2	Add finer controler over for hostremoval saving	2022-04-17 22:27:04 +02:00
James Fellows Yates	457c13e8b7	Add additional tips for host removal	2022-04-17 17:55:23 +02:00
James Fellows Yates	818d3bd053	Complete documentation for preprocessing subworkflows	2022-04-17 17:53:22 +02:00
James Fellows Yates	d0256ec937	Prettier	2022-04-16 07:45:24 +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	0e5c9e7bdd	Type:boolean for kaiju in nextflow_schema.json	2022-04-14 09:14:05 +02:00
sofstam	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	fc8a83245a	Add short-read host removal via BowTie2 alignment mapping ... Add short-read host removal via BowTie2 alignment mapping	2022-04-13 15:29:16 +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 A. Fellows Yates	67d94a9a8d	Merge pull request #45 from nf-core/run-merging ... Re-add run merging	2022-04-13 12:27:37 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James Fellows Yates	de57340526	Start work	2022-04-13 11:49:35 +02:00
James Fellows Yates	16a3556bfc	Changes after code review	2022-04-13 08:26:08 +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 Fellows Yates	a5f4fc42d5	Fix run merging for unmerged PE data	2022-04-12 09:25:27 +02:00
James A. Fellows Yates	1ac5a129a8	Merge pull request #52 from genomic-medicine-sweden/delete_extra_directory ... Delete extra unnecessary directory	2022-04-11 20:46:50 +02:00
sofstam	989dc55ce1	Delete extra nf-core directory	2022-04-11 17:42:38 +02:00
James Fellows Yates	78182c2a8c	Add comma	2022-04-11 13:40:24 +02:00
James Fellows Yates	ff2e508a38	Merge branch 'hostremoval' of github.com:nf-core/taxprofiler into hostremoval	2022-04-11 13:38:53 +02:00
James Fellows Yates	29073e3c93	Update CI tests	2022-04-11 13:38:42 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James A. Fellows Yates	fb2f5ed73e	Merge pull request #50 from nf-core/docs-prelim ... Initial attempt at adding usage docs	2022-04-11 10:52:18 +02:00
James A. Fellows Yates	b8b11fd065	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-11 10:30:29 +02:00
James Fellows Yates	b892fd0be5	Initial attempt at docs	2022-04-10 22:17:44 +02:00