138 commits

Author	SHA1	Message	Date
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +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	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	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
Thomas A. Christensen II	ad9bc4b7e9	Add the visualization workflow to the main workflow	2022-06-27 08:25:38 -05:00
James Fellows Yates	d48b3be5a7	Tweak DIAMOND save_reads message	2022-06-03 13:55:17 +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	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James A. Fellows Yates	a196e0f628	Merge branch 'dev' into add-filtlong	2022-06-02 11:51:26 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +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
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
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	5e6be52fab	Implement hostremoval	2022-05-03 09:34:27 +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	06b38f3699	Fix crash, add missing versions	2022-04-23 08:36:01 +02:00
James Fellows Yates	cda1274918	Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile	2022-04-23 06:47:59 +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	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 Fellows Yates	16a3556bfc	Changes after code review	2022-04-13 08:26:08 +02:00
James Fellows Yates	2ef21c6ef3	Fix input to profiling	2022-04-12 10:14:05 +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 Fellows Yates	78182c2a8c	Add comma	2022-04-11 13:40:24 +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	80c08af11b	Mix in profiling versions into mainline versons channel	2022-04-10 06:48:25 +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	afb66e445f	Append pairment to ID at profiling to prevent multiqc-level filename crash	2022-04-08 21:36:59 +02:00
James Fellows Yates	8839fe22b8	Fix output tuple for reads	2022-04-08 20:02:22 +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
James Fellows Yates	4d726a87e9	Fix metadata removal	2022-04-08 12:01:07 +02:00
James Fellows Yates	74c496f6af	Fix CAT_FASTQ output	2022-04-08 11:58:16 +02:00
James Fellows Yates	7b08c49cd6	Re-add run merging and gonna let GHA see if it works >.>	2022-04-08 11:54:54 +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	98f082d7b6	Fix mistake in previous upstream merge with AR2 output channel for settings file	2022-04-05 13:17:54 +02:00
James Fellows Yates	5b9355725d	Whoops	2022-04-05 13:14:06 +02:00
James Fellows Yates	245a4d1f5d	Fix MQC staging and remove debugging dump	2022-04-05 13:08:44 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +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
James Fellows Yates	469e4f3682	Remove remaining debugging .dumps(	2022-04-02 17:07:30 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	996b3f4912	fix: correct the input shape to metaphlan3	2022-04-02 15:00:26 +02:00
Moritz E. Beber	a425a322f2	refactor: make metaphlan3 run in workflow	2022-04-02 14:59:44 +02:00
Moritz E. Beber	69db920610	feat: include metaphlan3 in workflow	2022-04-02 14:59:44 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +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	ee53283696	Debugging comment	2022-03-28 09:13:05 +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
James Fellows Yates	120382f51d	Fix input channels to kraken2	2022-03-26 06:45:16 +01:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
James Fellows Yates	cc9368ee52	Prettier linting and update schema	2022-03-24 15:35:09 +01:00
James A. Fellows Yates	edce6603ef	Merge branch 'dev' into nf-core-template-merge-2.3.2	2022-03-24 14:10:58 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James Fellows Yates	8012998542	Make parameter naming more consistent for clipmerge	2022-03-21 19:52:50 +01:00
ljmesi	f6fe26de46	Rename shortread subworkflow to be more consistent	2022-03-21 18:25:56 +01:00
ljmesi	c97de32434	Make adapter and quality trimming optional	2022-03-21 18:17:08 +01:00
ljmesi	582aaa105f	Include long reads preprocessing subworkflow	2022-03-18 15:12:07 +01:00
Lauri Mesilaakso	0936b9b28e	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-03-18 14:18:38 +01:00
ljmesi	c8e49c56f4	Perform fastqc on nanopore reads before trimming	2022-03-18 13:47:44 +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	e39c6a8ccb	Fix MALT multiqc report clash	2022-03-03 18:04:03 +01:00
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	278f5605ca	Added database preparation and final channel for profiling	2022-02-19 12:36:08 +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