Closed LilyAnderssonLee closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 97c4c2b
+| ✅ 265 tests passed |+
!| ❗ 2 tests had warnings |!
The summary report from nanoq
generated by : nextflow run main.nf -profile test,singularity --outdir results/ --longread_filter_tool 'nanoq'
ERR3201952_ERR3201952_filtered.stats:
Nanoq Read Summary
====================
Number of reads: 2971
Number of bases: 6036813
N50 read length: 2205
Longest read: 11925
Shortest read: 1000
Mean read length: 2031
Median read length: 1741
Mean read quality: 8.57
Median read quality: 8.37
Read length thresholds (bp)
> 200 2971 100.0%
> 500 2971 100.0%
> 1000 2966 99.8%
> 2000 1155 38.9%
> 5000 55 01.9%
> 10000 1 00.0%
> 30000 0 00.0%
> 50000 0 00.0%
> 100000 0 00.0%
> 1000000 0 00.0%
Read quality thresholds (Q)
> 5 2971 100.0%
> 7 2971 100.0%
> 10 259 08.7%
> 12 70 02.4%
> 15 1 00.0%
> 20 0 00.0%
> 25 0 00.0%
> 30 0 00.0%
For the newly designed 1.2, should we include pychopper as an alterantive adapterermoval tool? Particuarly given as it's an official nanopore tool.
As Sofia mentioned in this issue, Pychopper was designed for cDNA reads. But I guess the principles for identifying and removing adapter sequences should be the same for both cDNA and DNA reads.
Another thing is Pychopper
was archived in 2022, and its last release was in 2020.
If you think it's proper, we could add it to 1.2 version.
@jfy133 It would be great if you could update metromap. I guess metromap could be updated in the end after adding all preprocessing tools for long reads.
For the newly designed 1.2, should we include pychopper as an alterantive adapterermoval tool? Particuarly given as it's an official nanopore tool.
As Sofia mentioned in this issue, Pychopper was designed for cDNA reads. But I guess the principles for identifying and removing adapter sequences should be the same for both cDNA and DNA reads.
Another thing is
Pychopper
was archived in 2022, and its last release was in 2020.If you think it's proper, we could add it to 1.2 version.
Ok if it's old and porechop_Abi is more recent we can stick with that
@jfy133 It would be great if you could update metromap. I guess metromap could be updated in the end after adding all preprocessing tools for long reads.
Yes lets update it right at the end, so I don't have to move everythign around every time :)
Add
nanoq
for nanopore reads filtering and nanopore reads summary statistics. Fix https://github.com/nf-core/taxprofiler/issues/415PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).