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sofstam 2023-02-03 15:54:29 +01:00
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4
docs/output.md
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@ -193,7 +193,7 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) and/
</details>
By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only see the mapped (host) and unmapped reads in `.bam` format or the off-target reads in .fastq format in your results directory if you provide `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped` respectively.
By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only see the mapped (host) and unmapped reads in `.bam` format or the off-target reads in `.fastq` format in your results directory if you provide `--save_hostremoval_mapped` and ` --save_hostremoval_unmapped` respectively.
> ⚠️ The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as run merging etc..
@ -229,7 +229,7 @@ By default, nf-core taxprofiler will only provide the `.bam` file containing map
</details>
This directory will be present and contain the unmapped reads from the FASTQ format from long-read minimap2 host removal (for short-read unmapped reads, see [bowtie2](#bowtie2), if `--save_hostremoval_unmapped` is supplied.
This directory will be present and contain the unmapped reads from the `.fastq` format from long-read minimap2 host removal (for short-read unmapped reads, see [bowtie2](#bowtie2)), if `--save_hostremoval_unmapped` is supplied.
### SAMtools stats

2
nextflow_schema.json
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@ -297,7 +297,7 @@
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "Saved mapped and unmapped reads in BAM format from host removal",
"help_text": "Save the reads mapped to the reference genome and offtarget reads in BAM format as output by the respective hostremoval alignment tool.\n\nThis can be useful if you wish to perform other analyses on the host organism (such as host-microbe interaction), however, you should consider whether the default mapping parameters of Bowtie2 (short-read) or minimap2 (long-read) are optimised to your context. "
"help_text": "Save the reads mapped to the reference genome and off-target reads in BAM format as output by the respective hostremoval alignment tool.\n\nThis can be useful if you wish to perform other analyses on the host organism (such as host-microbe interaction), however, you should consider whether the default mapping parameters of Bowtie2 (short-read) or minimap2 (long-read) are optimised to your context."
},
"save_hostremoval_unmapped": {
"type": "boolean",