mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:03:09 +00:00
Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
This commit is contained in:
parent
b892fd0be5
commit
b8b11fd065
2 changed files with 4 additions and 4 deletions
|
@ -36,7 +36,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
|
||||||
- Low complexity filtering ([bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus))
|
- Low complexity filtering ([bbduk](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/), [PRINSEQ++](https://github.com/Adrian-Cantu/PRINSEQ-plus-plus))
|
||||||
- Host read removal ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/))
|
- Host read removal ([BowTie2](http://bowtie-bio.sourceforge.net/bowtie2/))
|
||||||
- Run merging
|
- Run merging
|
||||||
3. Performs taxonomic profiling via a choice of any or all of:
|
3. Performs taxonomic profiling using one or more of:
|
||||||
- [Kraken2](https://ccb.jhu.edu/software/kraken2/)
|
- [Kraken2](https://ccb.jhu.edu/software/kraken2/)
|
||||||
- [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/)
|
- [MetaPhlAn3](https://huttenhower.sph.harvard.edu/metaphlan/)
|
||||||
- [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/)
|
- [MALT](https://uni-tuebingen.de/fakultaeten/mathematisch-naturwissenschaftliche-fakultaet/fachbereiche/informatik/lehrstuehle/algorithms-in-bioinformatics/software/malt/)
|
||||||
|
|
|
@ -20,7 +20,7 @@ This samplesheet is then specified on the command line as follows:
|
||||||
|
|
||||||
### Multiple runs of the same sample
|
### Multiple runs of the same sample
|
||||||
|
|
||||||
The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will processed reads before performing profiling. Below is an example for the same sample sequenced across 3 lanes:
|
The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will process reads before performing profiling. Below is an example for the same sample sequenced across 3 lanes:
|
||||||
|
|
||||||
```console
|
```console
|
||||||
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
|
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
|
||||||
|
@ -30,7 +30,7 @@ sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
|
||||||
|
|
||||||
```
|
```
|
||||||
|
|
||||||
> ⚠️ Runs of the sample sample sequenced on Illumina platforms with a combination of single and paired-end data will **not** be run-wise concatenated, unless pair-merging is specified. In the example above, `run3` will be profiled independently of `run1` and `run2` if pairs not merged.
|
> ⚠️ Runs of the same sample sequenced on Illumina platforms with a combination of single and paired-end data will **not** be run-wise concatenated, unless pair-merging is specified. In the example above, `run3` will be profiled independently of `run1` and `run2` if pairs are not merged.
|
||||||
|
|
||||||
### Full samplesheet
|
### Full samplesheet
|
||||||
|
|
||||||
|
@ -61,7 +61,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
|
||||||
|
|
||||||
nf-core/taxprofiler supports multiple databases being profiled in parallel for each tool. These databases, and specific parameters for each, can be specified in a 4 column comma-separated sheet.
|
nf-core/taxprofiler supports multiple databases being profiled in parallel for each tool. These databases, and specific parameters for each, can be specified in a 4 column comma-separated sheet.
|
||||||
|
|
||||||
> ⚠️ nf-core/taxprofiler does not provide any databases by default, nor currently generates them for you. This must be performed manually by the user.
|
> ⚠️ nf-core/taxprofiler does not provide any databases by default, nor does it currently generate them for you. This must be performed manually by the user.
|
||||||
|
|
||||||
An example database sheet can look as follows, where 4 tools are being used, and `malt` and `kraken2` will be used against two databases each.
|
An example database sheet can look as follows, where 4 tools are being used, and `malt` and `kraken2` will be used against two databases each.
|
||||||
|
|
||||||
|
|
Loading…
Reference in a new issue