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Fix docs links #107

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Sep 29, 2020
Merged

Fix docs links #107

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16f144a
Update link to kraken2 wiki
skrakau Sep 29, 2020
cadac17
Remove Documentation section from old template
skrakau Sep 29, 2020
215e034
Fix link to https://nf-co.re/mag
skrakau Sep 29, 2020
afa57be
Update link to kraken2 wiki about output formats
skrakau Sep 29, 2020
458e081
Add link to website for parameters section
skrakau Sep 29, 2020
1dc9ee2
Update usage.md
d4straub Sep 29, 2020
9ec3a4d
Update usage.md
d4straub Sep 29, 2020
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13 changes: 2 additions & 11 deletions README.md
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Expand Up @@ -17,7 +17,7 @@ It supports both short and long reads, quality trims the reads and adapters with

The pipeline then:

* assigns taxonomy to reads using [centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [kraken2](https://ccb.jhu.edu/software/kraken2/)
* assigns taxonomy to reads using [centrifuge](https://ccb.jhu.edu/software/centrifuge/) and/or [kraken2](https://github.com/DerrickWood/kraken2/wiki)
* performs assembly using [megahit](https://github.com/voutcn/megahit) and [spades](http://cab.spbu.ru/software/spades/), and checks their quality using [quast](http://quast.sourceforge.net/quast)
* performs metagenome binning using [metabat2](https://bitbucket.org/berkeleylab/metabat/src/master/), and checks the quality of the genome bins using [busco](https://busco.ezlab.org/)

Expand Down Expand Up @@ -51,16 +51,7 @@ See [usage docs](docs/usage.md) for all of the available options when running th

## Documentation

The nf-core/mag pipeline comes with documentation about the pipeline which you can read at [https://nf-core/mag/docs](https://nf-core/mag/docs) or find in the [`docs/` directory](docs).

1. [Installation](https://nf-co.re/usage/installation)
2. Pipeline configuration
* [Local installation](https://nf-co.re/usage/local_installation)
* [Adding your own system config](https://nf-co.re/usage/adding_own_config)
* [Reference genomes](https://nf-co.re/usage/reference_genomes)
3. [Running the pipeline](docs/usage.md)
4. [Output and how to interpret the results](docs/output.md)
5. [Troubleshooting](https://nf-co.re/usage/troubleshooting)
The nf-core/mag pipeline comes with documentation about the pipeline which you can read at [https://nf-co.re/mag](https://nf-co.re/mag) or find in the [`docs/` directory](docs).

## Credits

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4 changes: 2 additions & 2 deletions docs/output.md
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Expand Up @@ -92,7 +92,7 @@ Kraken2 classifies reads using a k-mer based approach as well as assigns taxonom

**Output directory: `Taxonomy/kraken2/[sample]`**

* `kraken2.report`: Classification in the Kraken report format. See the [kraken manual](http://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports) for more details
* `kraken2.report`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
* `taxonomy.krona.html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)

### Centrifuge
Expand All @@ -104,7 +104,7 @@ More information on the [Centrifuge](https://ccb.jhu.edu/software/centrifuge/) w
**Output directory: `Taxonomy/centrifuge/[sample]`**

* `report.txt`: Tab-delimited result file. See the [centrifuge manual](https://ccb.jhu.edu/software/centrifuge/manual.shtml#centrifuge-classification-output) for information about the fields
* `kreport.txt`: Classification in the Kraken report format. See the [kraken manual](http://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports) for more details
* `kreport.txt`: Classification in the Kraken report format. See the [kraken2 manual](https://github.com/DerrickWood/kraken2/wiki/Manual#output-formats) for more details
* `taxonomy.krona.html`: Interactive pie chart produced by [KronaTools](https://github.com/marbl/Krona/wiki)

### CAT
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2 changes: 2 additions & 0 deletions docs/usage.md
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Expand Up @@ -21,6 +21,8 @@ results # Finished results (configurable, see below)
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```

See the [nf-core/mag website documentation](https://nf-co.re/mag/usage#usage) for more information about pipeline specific parameters.

### Updating the pipeline

When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
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