millironx/taxprofiler
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1003 commits 7 branches 0 tags 7.5 MiB
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134 commits

Author SHA1 Message Date
James A. Fellows Yates
5a09319fb3
Merge branch 'dev' into multiqc-optimisations 2023-04-21 05:58:23 +02:00
James Fellows Yates
1eb951715f MultiQC optimisations for DIAMOND and Falco 2023-04-20 15:57:57 +02:00
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
James Fellows Yates
fbecfb6f33 Fix broken check for host read removal index 2023-03-17 20:47:09 +01:00
James Fellows Yates
5c549e5ce3 Remove TODOs and references to under development 2023-03-02 13:49:03 +01:00
James Fellows Yates
225773000f Fix channel structure when supplying own host bt2 index 2023-01-31 12:00:48 +01:00
James Fellows Yates
cac6f54d2d [extra] Fix warn related to recently changed parameter 2023-01-20 13:36:17 +01:00
James Fellows Yates
ab0c62bdc1 Post-release tweaks to usage.md 2022-12-23 16:23:29 +01:00
James A. Fellows Yates
acba31a8d6
Update taxprofiler.nf 2022-12-23 15:08:01 +01:00
James A. Fellows Yates
e586747680
Add missing comma to list 2022-12-23 15:06:26 +01:00
sofstam
6ebfdcd017 Add path parameters 2022-12-23 13:40:22 +01:00
Sofia Stamouli
d691b89727 Merge branch 'dev' into nf-core-template-merge-2.7.2 2022-12-20 15:14:41 +01:00
James A. Fellows Yates
25bb4304e8
Merge pull request #187 from nf-core/revert-pep 
Revert PEP validation back to python samplesheet check
 2022-12-20 15:03:18 +01:00
nf-core-bot
ab591e01ff Template update for nf-core/tools version 2.7.2 2022-12-19 12:10:58 +00:00
James Fellows Yates
07bd989bc6 Start work on groovy native datbase checks 2022-12-12 10:02:22 +01:00
James Fellows Yates
4b68e95770 Revert PEP validation back to python samplesheet check 2022-12-12 08:49:13 +01:00
James Fellows Yates
1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 2022-12-09 10:16:17 +01:00
nf-core-bot
36f3b5723b Template update for nf-core/tools version 2.7.1 2022-12-08 13:18:23 +00:00
Moritz E. Beber
4529e7e545 refactor: change parameter exclude unmerged to include 2022-12-04 21:36:12 +01:00
James A. Fellows Yates
1f31f88635
Merge pull request #158 from nf-core/adapterremoval-fix 
Fix adapterremoval adapter conflict and add optional adapter list file
 2022-11-03 11:36:14 +01:00
James Fellows Yates
d487a1ff2f Addd FASTP adadapter list 2022-11-02 12:39:34 +01:00
Sofia Stamouli
1bd6dbfe58 Add samtools stats for long-reads 2022-10-28 11:40:50 +02:00
Moritz E. Beber
bf89525bc2
Merge pull request #146 from nf-core/feat-bracken 
add Bracken to the profiling workflow
 2022-10-27 17:35:06 +02:00
James A. Fellows Yates
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Sofia Stamouli
d3d4297ca9 Apply review suggestions 2022-10-24 16:28:07 +02:00
Sofia Stamouli
511cb16a61 Apply review suggestions 2022-10-20 16:55:57 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
8768a16d63 refactor: turn warning into error 2022-10-17 17:35:41 +02:00
Moritz E. Beber
fd8a0df2a6 refactor: add warning when run_kraken2 is missing 2022-10-17 17:16:21 +02:00
Moritz E. Beber
fdb8a7f740 Merge branch 'devel' into nf-core-template-merge-2.6 2022-10-05 12:21:54 +02:00
nf-core-bot
51bacb00e6 Template update for nf-core/tools version 2.6 2022-10-05 03:30:53 +00:00
Rafal Stepien
bfd260e9c8 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-28 12:40:43 -04:00
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -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
cc5df924e4
Merge branch 'dev' into module-update 2022-09-08 13:36:21 +02:00
James Fellows Yates
fc26948950 Fix MultiQC 2022-09-08 12:49:38 +02:00
James Fellows Yates
d11257b330 Module update 2022-09-08 08:08:36 +02:00
James Fellows Yates
bbd8049ca1 Remove duplicated multqic mixing 2022-09-07 13:44:08 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James Fellows Yates
5552c264b9 Remove now unnecessary input validation 2022-08-30 14:14:01 +02:00
James Fellows Yates
8917e29e35 Fix accidental overly zelous search-and-replace 2022-08-30 14:11:48 +02:00
James Fellows Yates
3f8f32cba8 Make longread quality ftilering opt out 2022-08-30 14:08:05 +02:00
James Fellows Yates
2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests 2022-08-30 13:58:58 +02:00
James Fellows Yates
139cf0d6aa Fix 2022-07-26 10:12:33 +02:00
James A. Fellows Yates
cc3967a3fd
Apply suggestions from code review 2022-07-15 10:51:41 +02:00
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