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Apply suggestions from code review
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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@ -255,13 +255,13 @@ This directory will be present and contain the unmapped reads from the `.fastq`
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<summary>Output files</summary>
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- `samtoolsstats`
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- `<sample_id>_{fq,fastq}.gz`: Final reads that underwent preprocessing that were sent for classification/profiling.
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- `<sample_id>_{fq,fastq}.gz`: Final reads that underwent preprocessing and were sent for classification/profiling.
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</details>
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The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the \_last step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - this will be the ones present in this directory.
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The results directory will contain the 'final' processed reads used as input for classification/profiling. It will _only_ include the output of the \_last step of any combinations of preprocessing steps that may have been specified in the run configuration. For example, if you perform the read QC and host-removal preprocessing steps, the final reads that are sent to classification/profiling are the host-removed FASTQ files - those will be the ones present in this directory.
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> ⚠️ If you turn off all preprocessing steps, then no results will be present in this directory. This happens independtly for short- and long-reads. I.e. you will only have FASTQ files for short reads in this directory if you skip all long-read preprocessing.
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> ⚠️ If you turn off all preprocessing steps, then no results will be present in this directory. This happens independently for short- and long-reads. I.e. you will only have FASTQ files for short reads in this directory if you skip all long-read preprocessing.
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### SAMtools stats
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@ -293,7 +293,7 @@ This is the last possible preprocessing step, so if you have multiple runs or li
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Note that you will only find samples that went through the run merging step in this directory. For samples that had a single run or library will not go through this step of the pipeline and thus will not be present in this directory.
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This directory and it's FASTQ files will only be present if you supply `--save_runmerged_reads`.Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
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This directory and its FASTQ files will only be present if you supply `--save_runmerged_reads`.Alternatively, if you wish only to have the 'final' reads that go into classification/profiling (i.e., that may have additional processing), do not specify this flag but rather specify `--save_analysis_ready_reads`, in which case the reads will be in the folder `analysis_ready_reads`.
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### Bracken
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