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712 commits 7 branches 0 tags 7.5 MiB
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125 commits

Author SHA1 Message Date
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
James Fellows Yates
80c08af11b Mix in profiling versions into mainline versons channel 2022-04-10 06:48:25 +02:00
James Fellows Yates
082093f3de Prettier 2022-04-10 06:44:10 +02:00
James Fellows Yates
ecf0eea4f9 Move profiling to subworkflow and standardise outputs 2022-04-10 06:43:30 +02:00
James Fellows Yates
afb66e445f Append pairment to ID at profiling to prevent multiqc-level filename crash 2022-04-08 21:36:59 +02:00
James Fellows Yates
8839fe22b8 Fix output tuple for reads 2022-04-08 20:02:22 +02:00
James Fellows Yates
ca011ccc5b Fix cat_fastq naming logic? 2022-04-08 13:28:37 +02:00
James Fellows Yates
d130a72d74 Get this working 2022-04-08 13:09:23 +02:00
James Fellows Yates
4d726a87e9 Fix metadata removal 2022-04-08 12:01:07 +02:00
James Fellows Yates
74c496f6af Fix CAT_FASTQ output 2022-04-08 11:58:16 +02:00
James Fellows Yates
7b08c49cd6 Re-add run merging and gonna let GHA see if it works >.> 2022-04-08 11:54:54 +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
98f082d7b6 Fix mistake in previous upstream merge with AR2 output channel for settings file 2022-04-05 13:17:54 +02:00
James Fellows Yates
5b9355725d Whoops 2022-04-05 13:14:06 +02:00
James Fellows Yates
245a4d1f5d Fix MQC staging and remove debugging dump 2022-04-05 13:08:44 +02:00
James A. Fellows Yates
3d662d2e06
Merge branch 'dev' into complexity-filter-bbduk 2022-04-04 21:19:36 +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
469e4f3682 Remove remaining debugging .dumps( 2022-04-02 17:07:30 +02:00
James Fellows Yates
b055df5ea0 Add bbduk complexity (entropy-based) filtering 2022-04-02 17:02:05 +02:00
Moritz E. Beber
996b3f4912 fix: correct the input shape to metaphlan3 2022-04-02 15:00:26 +02:00
Moritz E. Beber
a425a322f2 refactor: make metaphlan3 run in workflow 2022-04-02 14:59:44 +02:00
Moritz E. Beber
69db920610 feat: include metaphlan3 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 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
ee53283696 Debugging comment 2022-03-28 09:13:05 +02:00
James Fellows Yates
8dc9e583ad Debugging run merging 2022-03-27 09:30:23 +02:00
James A. Fellows Yates
e6e8ed7cc9 Add some debugging notes 2022-03-26 20:54:50 +00:00
James Fellows Yates
120382f51d Fix input channels to kraken2 2022-03-26 06:45:16 +01:00
sofstam
37a70dc3e3 Merge branch 'dev' into classification_centrifuge 2022-03-25 16:18:35 +01:00
James Fellows Yates
4e93abc7c0 Add read improved read preprocessing 2022-03-25 14:58:06 +01:00
James Fellows Yates
cc9368ee52 Prettier linting and update schema 2022-03-24 15:35:09 +01:00
James A. Fellows Yates
edce6603ef
Merge branch 'dev' into nf-core-template-merge-2.3.2 2022-03-24 14:10:58 +01:00
sofstam
3ff54e620e Add centrifuge classification 2022-03-24 13:02:25 +01:00
nf-core-bot
6b939e6728 Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00
James Fellows Yates
81bfb629ca Add working basic test to begin 2022-03-21 20:28:09 +01:00
James Fellows Yates
8012998542 Make parameter naming more consistent for clipmerge 2022-03-21 19:52:50 +01:00
ljmesi
f6fe26de46 Rename shortread subworkflow to be more consistent 2022-03-21 18:25:56 +01:00
ljmesi
c97de32434 Make adapter and quality trimming optional 2022-03-21 18:17:08 +01:00
ljmesi
582aaa105f Include long reads preprocessing subworkflow 2022-03-18 15:12:07 +01:00
Lauri Mesilaakso
0936b9b28e
Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-03-18 14:18:38 +01:00
ljmesi
c8e49c56f4 Perform fastqc on nanopore reads before trimming 2022-03-18 13:47:44 +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
e39c6a8ccb Fix MALT multiqc report clash 2022-03-03 18:04:03 +01:00
James Fellows Yates
2c183ed2ed Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue) 2022-03-03 17:42:02 +01:00
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