203 commits

Author	SHA1	Message	Date
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
James Fellows Yates	d3572e1878	Final MQC fix for AR2 (remove too-early collect)	2022-04-03 07:28:01 +02:00
Moritz E. Beber	f5baf910be	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-04-03 00:21:09 +02:00
Moritz E. Beber	be93eae640	fix: insert .fastq file extension ... The MetaPhlAn3 module computes the input type from the file extension without the possibility to configure an override. Since AdapterRemoval2 creates files without `.fastq` extensions, MetaPhlAn3 input was determined to be SAM.	2022-04-02 21:50:13 +02:00
Moritz E. Beber	4eab257d68	style: prettify comment	2022-04-02 17:05:46 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	a425a322f2	refactor: make metaphlan3 run 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 A. Fellows Yates	03e832954f	Update subworkflows/local/shortread_adapterremoval.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 20:55:33 +02:00
James A. Fellows Yates	14f2b7bd84	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 15:34:05 +02:00
James Fellows Yates	dcda815bfb	Add final adapterremoval options to match fastp functionality	2022-04-01 09:50:08 +02:00
James Fellows Yates	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +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	8dc9e583ad	Debugging run merging	2022-03-27 09:30:23 +02:00
James A. Fellows Yates	622fafedc8	Prempt centrifuge database untar crash	2022-03-26 20:22:35 +00:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James A. Fellows Yates	000f129dab	Apply suggestions from code review	2022-03-25 15:32:56 +01:00
James Fellows Yates	ede362dbf9	Remove duplicate config and sync longread fastqc	2022-03-25 15:28:30 +01:00
James Fellows Yates	b763bfa2c0	More cleanup	2022-03-25 15:26:57 +01:00
James Fellows Yates	0e6f7e2ca1	Revert "Some more cleanup" ... This reverts commit 7ddcb09a85.	2022-03-25 15:24:10 +01:00
James Fellows Yates	7ddcb09a85	Some more cleanup	2022-03-25 15:22:41 +01:00
James Fellows Yates	b5f5c75504	Fix file header descriptions	2022-03-25 15:21:52 +01:00
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	07eed435c6	Replace set with explicity assignment	2022-03-21 19:54:51 +01:00
James Fellows Yates	8012998542	Make parameter naming more consistent for clipmerge	2022-03-21 19:52:50 +01:00
ljmesi	5b1b48e59e	Update subworkflow name to be more consistent	2022-03-21 18:29:47 +01:00
ljmesi	f6fe26de46	Rename shortread subworkflow to be more consistent	2022-03-21 18:25:56 +01:00
James A. Fellows Yates	631c115e10	Adds PoC of untarring system	2022-03-21 14:58:19 +00:00
James Fellows Yates	c7f022008c	Start getting database prep ready	2022-03-21 15:07:59 +01:00
ljmesi	1e42f1d9f2	Add long read preprocessing subworkflow	2022-03-18 15:10:44 +01:00
ljmesi	41b3d8db82	Add nanopore channel	2022-03-18 10:47:41 +01:00
ljmesi	0f0ed6cd46	Fix function name	2022-03-18 10:45:06 +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	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