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James Fellows Yates 2023-01-31 13:07:07 +01:00
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docs/output.md
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@ -71,7 +71,7 @@ It is used in nf-core/taxprofiler for adapter trimming of short-reads.
</details>
By default nf-core/taxprofiler will only provide the `<sample_id>.fastp.fastq.gz` file if fastp is selected. The file `<sample_id>.merged.fastq.gz` will be available in the output folder if you provide the argument ` --shortread_qc_mergepairs` (optionally retaining un-merged pairs when in combination with `--shortread_qc_includeunmerged`).
By default nf-core/taxprofiler will only provide the `<sample_id>.fastp.fastq.gz` file if fastp is selected. The file `<sample_id>.merged.fastq.gz` will be available in the output folder if you provide the argument ` --shortread_qc_mergepairs` (optionally retaining un-merged pairs when in combination with `--shortread_qc_includeunmerged`).
You can change the default value for low complexity filtering by using the argument `--shortread_complexityfilter_fastp_threshold`.
@ -93,7 +93,7 @@ You can change the default value for low complexity filtering by using the argum
</details>
By default nf-core/taxprofiler will only provide the `.settings` file if AdapterRemoval is selected.
By default nf-core/taxprofiler will only provide the `.settings` file if AdapterRemoval is selected.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_reads`. If this is selected, you may receive different combinations of `.fastq` files for each sample depending on the input types - e.g. whether you have merged or not, or if you're supplying both single- and paired-end reads.
@ -112,9 +112,9 @@ You will only find the `.fastq` files in the results directory if you provide `
</details>
The output logs are saved in the output folder and are part of MultiQC report.You do not normally need to check these manually.
The output logs are saved in the output folder and are part of MultiQC report.You do not normally need to check these manually.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_reads`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_reads`.
> ⚠️ We do **not** recommend using Porechop if you are already trimming the adapters with ONT's basecaller Guppy.
@ -169,9 +169,9 @@ By default nf-core/taxprofiler will only provide the `.log` file if PRINSEQ++ is
</details>
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_reads`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_reads`.
> ⚠️ We do **not** recommend using Filtlong if you are performing filtering of low quality reads with ONT's basecaller Guppy.
> ⚠️ We do **not** recommend using Filtlong if you are performing filtering of low quality reads with ONT's basecaller Guppy.
### Bowtie2
@ -334,7 +334,7 @@ The most summary file is the `*combined_reports.txt` file which summarises resul
</details>
By default you will receive a TSV output. Alternatively, you will receive a `*.sam` file if you provide the parameter `--diamond_save_reads` but in this case no taxonomic classification will be available(!), only the aligned reads in sam format.
By default you will receive a TSV output. Alternatively, you will receive a `*.sam` file if you provide the parameter `--diamond_save_reads` but in this case no taxonomic classification will be available(!), only the aligned reads in sam format.
> ℹ️ DIAMOND has many output formats, so depending on your [choice](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options) with ` --diamond_output_format` you will receive the taxonomic information in a different format.
@ -425,7 +425,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
All tools in taxprofiler supported by MultiQC will have a dedicated section showing summary statistics of each tool based on information stored in log files.
All tools in taxprofiler supported by MultiQC will have a dedicated section showing summary statistics of each tool based on information stored in log files.
> ℹ️ The 'General Stats' table by default will only show statistics referring to pre-processing steps, and will not display possible values from each classifier/profiler, unless turned on by the user within the 'Configure Columns' menu or via a custom MultiQC config file (`--multiqc_config`)