68 commits

Author	SHA1	Message	Date
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