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279 commits

Author SHA1 Message Date
Moritz E. Beber
563b34c9c3 refactor: rename process to kraken2 2022-10-14 14:48:27 +02:00
Moritz E. Beber
95621ebd8a fix: include local module 2022-10-14 14:47:08 +02:00
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
James Fellows Yates
56bae85755 Remove necessity of patch 2022-10-11 12:38:18 +02:00
Moritz E. Beber
180cac0395 fix: adapt to new samtools/view input 2022-10-05 13:49:35 +02:00
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +02:00
James A. Fellows Yates
3ca9058b9c
Merge pull request #133 from rafalstepien/add-pep-support 
Add working version of PEP-nf-core integration
 2022-09-30 10:21:15 +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
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00
James A. Fellows Yates
f43c54317c
Update subworkflows/local/standardisation_profiles.nf 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2022-09-16 15:20:47 +02:00
James Fellows Yates
c5cc21d29e Update motus merge module to remove unused channel 2022-09-16 10:25:24 +02:00
James Fellows Yates
4e7857e2ed Standardise mOTUs table merge 2022-09-16 08:36:34 +02:00
Rafal Stepien
768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules 2022-09-15 12:31:49 -04:00
James A. Fellows Yates
cdb21d17b3
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-15 13:08:57 +02:00
James Fellows Yates
21ae9d85c3 Ensure merge metaphlan3 tables happens on per database basis 2022-09-15 12:29:54 +02:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James Fellows Yates
05e9d92444 Add centrigue kreports 2022-09-13 16:47:19 +02:00
James Fellows Yates
c8dbf5be47 Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU 2022-09-13 15:47:28 +02:00
James Fellows Yates
a764bc4807 Start works - need updated module though t have meta 2022-09-09 13:57:06 +02:00
James A. Fellows Yates
cc5df924e4
Merge branch 'dev' into module-update 2022-09-08 13:36:21 +02:00
James Fellows Yates
d11257b330 Module update 2022-09-08 08:08:36 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James A. Fellows Yates
8456f934ed
Update subworkflows/local/visualization_krona.nf 2022-09-02 16:15:46 +02:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
James Fellows Yates
d19a473c59 Merge branch 'filtlong-in-tests' into json-schema 2022-08-30 14:33:19 +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
d4af88e3ff Make kaiju parameter clearer for documentation purpses and update documentation 2022-08-25 15:50:28 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00
James A. Fellows Yates
f48b22d615
Apply suggestions from code review 2022-07-29 09:52:49 +02:00
James Fellows Yates
873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log 2022-07-29 09:51:34 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update 2022-07-28 15:48:59 +02:00
sofstam
cecbb41f88 Update centrifuge/kreport 2022-07-27 14:42:35 +02:00
James A. Fellows Yates
9d2be68fb8 Merge branch 'dev' into centrifuge_mqc 2022-07-26 18:01:30 +00:00
James A. Fellows Yates
1ef0975736 Merge branch 'dev' into porechop-log 2022-07-26 18:00:28 +00:00
James A. Fellows Yates
3054dea7c2 Get multiqc input working 2022-07-26 08:41:06 +00:00
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00
James Fellows Yates
139cf0d6aa Fix 2022-07-26 10:12:33 +02:00
James A. Fellows Yates
64f01fcfe0
Merge branch 'dev' into porechop-log 2022-07-20 14:05:23 +02:00
James Fellows Yates
255afee4c7 Re-add the collects 2022-07-19 17:10:10 +02:00
Mahwash Jamy
811ded38af
Update subworkflows/local/profiling.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-07-19 16:44:48 +02:00
Sofia Stamouli
237e9aa623
Update longread_preprocessing.nf 2022-07-19 16:44:08 +02:00
James A. Fellows Yates
8d7ddb5847
Apply suggestions from code review 2022-07-19 16:30:13 +02:00
mjamy
c4c82212e1 incorporate diamond log file into multiqc channel 2022-07-19 14:12:16 +02:00
sofstam
171258d545 Fix typos 2022-07-19 14:07:13 +02:00
sofstam
25bc01f9c4 Fix typos 2022-07-19 14:04:49 +02:00
sofstam
8147dba0b4 Fix typos 2022-07-19 14:03:10 +02:00
sofstam
526ed79763 Fix filtlong logs 2022-07-19 14:01:11 +02:00
sofstam
1ba6a08135 Seperate multiqc for filtlong 2022-07-19 13:53:29 +02:00
James Fellows Yates
33a5402b25 Add emitting porechop logs to multiqc and fix collection of others 2022-07-19 13:50:39 +02:00
sofstam
3f5fa8cc7a Merge branch 'dev' into update_filtlong 2022-07-19 13:50:28 +02:00
sofstam
5a2fd260fd Log file into multiqc channel 2022-07-15 12:50:50 +02:00
James A. Fellows Yates
c215ed5607
Merge branch 'dev' into motus/merge 2022-07-15 10:52:42 +02:00
James A. Fellows Yates
cc3967a3fd
Apply suggestions from code review 2022-07-15 10:51:41 +02:00
James Fellows Yates
31119f83c2 Send to MQC only the log file not the meta 2022-07-13 14:29:47 +02:00
James Fellows Yates
13280e2468 Fix .empty 2022-07-13 12:44:44 +02:00
James Fellows Yates
eaa69b65d8 Update mOTUs profile module and mix log for multiqc 2022-07-13 12:38:30 +02:00
James Fellows Yates
c22946cfab Fix motu versions not being exported if not run 2022-07-13 12:36:29 +02:00
James Fellows Yates
a0ee82bf43 Add motus/merge and biom support 2022-07-12 11:39:26 +02:00
James A. Fellows Yates
8082c7d108
Merge pull request #97 from nf-core/malt-to-krona 
Add Krona support for MALT
 2022-07-05 15:17:52 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus 2022-07-04 13:14:42 +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
James Fellows Yates
27f174d17e Merge remote-tracking branch 'origin/dev' into malt-to-krona 2022-06-30 12:01:33 +02:00
James Fellows Yates
0050f45345 Add taxonomy directory param 2022-06-30 11:43:52 +02:00
Thomas A. Christensen II
6673ccf8d8
Update channel assignment alignment in profiling subworkflow 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-28 09:00:43 -05:00
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
23fec89b06
Add Krona chart creation for Centrifuge reports 2022-06-27 08:52:29 -05:00
Thomas A. Christensen II
a40a442178
Create VISUALIZATION_KRONA workflow to create Krona charts 2022-06-27 08:22:47 -05:00
James Fellows Yates
e0ad49ebc9 Fix metadata manipulaton for malt 2022-06-10 19:33:37 +02:00
James A. Fellows Yates
621b6a3d09
Add comments about MALT id replacement and refactor for simplicity 2022-06-10 11:27:51 +02:00
James A. Fellows Yates
ebdd5683b2
Apply suggestions from code review 2022-06-03 22:33:48 +02:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads 2022-06-03 13:48:54 +02:00
James A. Fellows Yates
53c4399052
Merge branch 'dev' into motus 2022-06-02 21:38:35 +02:00
James A. Fellows Yates
c9581b1796
Merge branch 'dev' into support-aligned-reads 2022-06-02 12:45:29 +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
JIANHONG OU
4b3216c1cb filter fasta inputs for mOTUs; 
fix the typo for nopreprocessing in nextflow.config.
 2022-05-24 08:42:18 -04:00
JIANHONG OU
68d0cc00fa add motus profile. 2022-05-23 08:05:06 -04:00
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
James A. Fellows Yates
e7b54801ed
Merge pull request #75 from nf-core/improve-error-message 
Only create profiler input channels when profiler activated
 2022-05-06 11:51:33 +02:00
ljmesi
5e6be52fab Implement hostremoval 2022-05-03 09:34:27 +02:00
James Fellows Yates
d5049a34e4 Add missing close bracket 2022-05-01 07:28:29 +02:00
James Fellows Yates
4094706421 Only create profiler input channels when profiler activate 2022-05-01 07:24:58 +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
8126d16dee Add draft version of DIAMOND 2022-04-29 21:59:42 +02:00
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
James A. Fellows Yates
bc84afe80d
Merge pull request #66 from nf-core/versions-fix 
Fix version reporting
 2022-04-25 16:38:28 +02:00
James Fellows Yates
06b38f3699 Fix crash, add missing versions 2022-04-23 08:36:01 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
Sofia Stamouli
e71e7b86a2
Merge pull request #53 from genomic-medicine-sweden/classification_kaiju 
Add kaiju/kaiju in taxprofiler
 2022-04-20 10:57:00 +02:00
Sofia Stamouli
236141f065 Resolve conflicts with dev 2022-04-20 10:17:10 +02:00
James A. Fellows Yates
571495c812
Merge pull request #60 from nf-core/fasta-filtering 
Adds filtering out of FASTA for tools that don't support it
 2022-04-20 10:11:17 +02:00
James Fellows Yates
9fd94b1389 Switch to string interpolation 2022-04-20 09:25:54 +02:00
James Fellows Yates
60d232d62c Revert "Update subworkflows/local/profiling.nf" 
This reverts commit b7d0557ee0.
 2022-04-20 09:23:38 +02:00
James A. Fellows Yates
b7d0557ee0
Update subworkflows/local/profiling.nf 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-20 09:15:45 +02:00
James A. Fellows Yates
87777a4289
Update subworkflows/local/profiling.nf 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-04-19 12:54:57 +02:00
James A. Fellows Yates
ecaff371aa
Update input_check.nf 2022-04-18 07:35:19 +02:00
James A. Fellows Yates
9f634805e4
Update subworkflows/local/profiling.nf 2022-04-18 07:31:44 +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
cc73cdd51d Add generation of taxon-table like output for MALT 2022-04-16 07:42:30 +02:00
James A. Fellows Yates
6fecb3eeb7
Merge pull request #54 from nf-core/dev 
Get upstream changes
 2022-04-16 06:17:33 +02:00
sofstam
68ce5843a4 Add kaiju in taxprofiler 2022-04-13 18:51:56 +02:00
James A. Fellows Yates
70f94603b0
Merge branch 'dev' into hostremoval 2022-04-13 13:59:51 +02:00
James Fellows Yates
de57340526 Start work 2022-04-13 11:49:35 +02:00
James Fellows Yates
a15c45b00c Put map in the rigt place 2022-04-12 10:51:27 +02:00
James Fellows Yates
8d68914192 Re-add operator name 2022-04-12 10:47:44 +02:00
James Fellows Yates
26399718b2 Re-add pairment attachment 2022-04-12 10:46:03 +02:00
James Fellows Yates
2ef21c6ef3 Fix input to profiling 2022-04-12 10:14:05 +02:00
James Fellows Yates
9f221f84cc Only supply single input channel to profiling, as these are merged into single input channel at run_merging 2022-04-12 10:12:17 +02:00
James A. Fellows Yates
967b1f7d6e
Merge branch 'dev' into run-merging 2022-04-12 09:28:10 +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
ecf0eea4f9 Move profiling to subworkflow and standardise outputs 2022-04-10 06:43:30 +02:00
James Fellows Yates
35cb6e042a Flatten the right thing 2022-04-08 13:46:12 +02:00
James Fellows Yates
6c14f2b230 Remove the flattening? 2022-04-08 13:44:52 +02:00
James Fellows Yates
a634814d84 Formatting and fix fastp output 2022-04-08 13:34:00 +02:00
James Fellows Yates
d130a72d74 Get this working 2022-04-08 13:09:23 +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
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