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Co-authored-by: Sateesh_Peri <[email protected]>
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jfy133 and sateeshperi authored Dec 16, 2024
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4 changes: 2 additions & 2 deletions docs/output.md
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Expand Up @@ -111,7 +111,7 @@ The pipeline uses Nanolyse to map the reads against the Lambda phage and removes

### Long read adapter removal

The pipeline uses porecho_abi or porechop to perform adaptertrimming of the long reads that are eventually provided with the TSV input file.
The pipeline uses porecho_abi or porechop to perform adapter trimming of the long reads that are eventually provided with the TSV input file.

<details markdown="1">
<summary>Output files</summary>
Expand All @@ -138,7 +138,7 @@ The pipeline uses filtlong, chopper, or nanoq for quality filtering of long read

</details>

Trimmed and filtered FASTQ output directories and files will only exist if `--save_porechop_reads` and/or `--save_filtered_longreads` (respectively) are provided to the run command .
Trimmed and filtered FASTQ output directories and files will only exist if `--save_porechop_reads` and/or `--save_filtered_longreads` (respectively) are provided to the run command.

No direct host read removal is performed for long reads.
However, since within this pipeline filtlong uses a read quality based on k-mer matches to the already filtered short reads, reads not overlapping those short reads might be discarded. Note that this only applies when using filtlong as long read filtering tool.
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3 changes: 1 addition & 2 deletions nextflow.config
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Expand Up @@ -385,7 +385,6 @@ manifest {
name = 'nf-core/mag'
author = """Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
contributors = [
// TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
[
name: 'Hadrien Gourlé',
affiliation: 'Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Swden',
Expand Down Expand Up @@ -446,7 +445,7 @@ manifest {
name: 'Carson Miller',
affiliation: 'University of Washington, Seattle, USA',
email: '0000-0002-7175-0533',
github: 'prototaxites',
github: 'CarsonJM',
contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')
orcid: '0000-0001-9861-4884'
],
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