Sofia Stamouli
236141f065
Resolve conflicts with dev
2022-04-20 10:17:10 +02:00
James A. Fellows Yates
87777a4289
Update subworkflows/local/profiling.nf
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Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-04-19 12:54:57 +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
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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
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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
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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
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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
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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
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
8dc9e583ad
Debugging run merging
2022-03-27 09:30:23 +02:00
James A. Fellows Yates
622fafedc8
Prempt centrifuge database untar crash
2022-03-26 20:22:35 +00:00
sofstam
37a70dc3e3
Merge branch 'dev' into classification_centrifuge
2022-03-25 16:18:35 +01:00