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469 commits 7 branches 0 tags 7.5 MiB
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102 commits

Author SHA1 Message Date
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
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