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Add chopper and nanoq options for longread preprocessing

5

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

muabnezor

Optional skipping of short-read input to Filtlong for large datasets

1

### Description of the bug Hi all - long time listener first time caller: I have a rather large set of Illumina data along with some nanopore reads on which...

ddomman

Create a samplesheet for funcscan

1

### Description of feature This would generate a samplesheet that is directly compatible with funcscan.

jasmezz

vagkaratzas

### Description of feature https://www.nature.com/articles/s41587-023-01983-6#Sec9 Also works on ONT pretty well in some cases (although better after polishing)

jfy133

### Description of feature As added in nf-core/taxprofiler https://github.com/nf-core/taxprofiler/tree/bouncy-basenji

jfy133

### Description of feature To address this: https://github.com/nf-core/mag/issues/275 A good first (best performing) nanopore assembler is Flye

jfy133

Update metaspades to 4.0.0

1

### Description of the bug Bioconda recipe currently broken for SPAdes 3.15.5, updated to 4.0.0 is reported to fix the issue. Discussed on slack in this thread: https://nfcore.slack.com/archives/CE9MS66BS/p1721298005029789 ### Command...

elsherbini

convert_depths for co-assembly taking only average depth and not sample wise read depths for maxbin2 binning with solution

2

### Description of the bug I ran into the issue of not generating high quality bins for a known bacteria present in my samples (0.25 by DASTool scoring) when using...

uel3

### Description of feature https://www.biorxiv.org/content/10.1101/2024.08.09.607291v1.full Thanks to @ivelsko for making me aware!

jfy133