millironx/taxprofiler
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32 commits

Author SHA1 Message Date
James A. Fellows Yates
03c3169f10 Replace all instance of exit 1 with error for safety and consistency 2023-04-04 09:41:22 +00:00
Moritz E. Beber
bb7323e25d fix: restore setting id on FASTQ meta 2023-03-11 11:34:47 +01:00
Moritz E. Beber
fa1c779536 fix: insert id key again 2023-03-11 11:28:42 +01:00
Moritz E. Beber
d17dce5590 style: use subMap and early returns 2023-03-11 11:28:42 +01:00
Moritz E. Beber
0bcea6c993 style: use parameter for branch closure 2023-03-11 11:28:42 +01:00
James Fellows Yates
577da7e835 Remove .first() as the module only executes once anyway and we get a ugly warning 2022-12-20 13:59:14 +01:00
James Fellows Yates
11db981a88 minor fixes 2022-12-20 13:55:15 +01:00
James A. Fellows Yates
7709245874
Update subworkflows/local/input_check.nf 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-12-20 13:54:05 +01:00
James Fellows Yates
4b68e95770 Revert PEP validation back to python samplesheet check 2022-12-12 08:49:13 +01:00
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +02:00
James Fellows Yates
87edc4569c Move to a function 2022-09-27 15:46:17 +02:00
James Fellows Yates
43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead 2022-09-27 15:32:51 +02:00
Rafal Stepien
1584d6fc51 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 10:43:04 -04:00
Rafal Stepien
768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules 2022-09-15 12:31:49 -04:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James A. Fellows Yates
ecaff371aa
Update input_check.nf 2022-04-18 07:35:19 +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
sofstam
d897c922b2 Add centrifuge classificatioN 2022-04-04 13:51:51 +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
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
c7f022008c Start getting database prep ready 2022-03-21 15:07:59 +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