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Mar 12, 2025
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Switch from using save_analysis_ready_reads to save_analysis_ready_fa… #586

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Switch from using save_analysis_ready_reads to save_analysis_ready_fa…
epstein6 Mar 11, 2025
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Update CHANGELOG.md
epstein6 Mar 12, 2025
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Merge branch 'dev' into fix_docs_saves
LilyAnderssonLee Mar 12, 2025
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Update README.md
epstein6 Mar 12, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#573](https://github.com/nf-core/taxprofiler/pull/573) Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133)
- [#578](https://github.com/nf-core/taxprofiler/pull/578) Fixed incorrect keyword in nextflow_schema.json (fix by @mashehu)
- [#585](https://github.com/nf-core/taxprofiler/pull/585) Fixed code blocks (fix by @masheshu)
- [#586](https://github.com/nf-core/taxprofiler/pull/586) Fixed wrong argument name for saving analysis reads (fix by @epstein6)

### `Dependencies`

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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -121,6 +121,7 @@ We thank the following people for their contributions to the development of this
- [Rafal Stepien](https://github.com/rafalstepien)
- [Mahwash Jamy](https://github.com/mjamy)
- [Alex Caswell](https://github.com/AlexHoratio)
- [Aidan Epstein](https://github.com/epstein6)

### Acknowledgments

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22 changes: 11 additions & 11 deletions docs/output.md
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Expand Up @@ -120,7 +120,7 @@ You can change the default value for low complexity filtering by using the argum

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. 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`.
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. 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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::warning
The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as complexity filtering, host removal, run merging etc..
Expand Down Expand Up @@ -164,7 +164,7 @@ The `.npo` files can be used for re-generating and customising the plots using t

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`. 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`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::warning
We do **not** recommend using Porechop if you are already trimming the adapters with ONT's basecaller Guppy.
Expand All @@ -185,7 +185,7 @@ We do **not** recommend using Porechop if you are already trimming the adapters

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`. 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`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

### BBDuk

Expand All @@ -202,7 +202,7 @@ It is used in nf-core/taxprofiler for complexity filtering using different algor

</details>

By default nf-core/taxprofiler will only provide the `.log` file if BBDuk is selected as the complexity filtering tool. You will only find the complexity filtered reads in your results directory if you provide ` --save_complexityfiltered_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`.
By default nf-core/taxprofiler will only provide the `.log` file if BBDuk is selected as the complexity filtering tool. You will only find the complexity filtered reads in your results directory if you provide ` --save_complexityfiltered_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::warning
The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as host removal, run merging etc..
Expand All @@ -223,7 +223,7 @@ It is used in nf-core/taxprofiler for complexity filtering using different algor

</details>

By default nf-core/taxprofiler will only provide the `.log` file if PRINSEQ++ is selected as the complexity filtering tool. You will only find the complexity filtered `.fastq` files in your results directory if you supply ` --save_complexityfiltered_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`.
By default nf-core/taxprofiler will only provide the `.log` file if PRINSEQ++ is selected as the complexity filtering tool. You will only find the complexity filtered `.fastq` files in your results directory if you supply ` --save_complexityfiltered_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::warning
The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as host removal, run merging etc..
Expand All @@ -242,7 +242,7 @@ The resulting `.fastq` files may _not_ always be the 'final' reads that go into

</details>

You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::warning
We do _not_ recommend using Filtlong if you are performing filtering of low quality reads with ONT's basecaller Guppy.
Expand All @@ -261,7 +261,7 @@ We do _not_ recommend using Filtlong if you are performing filtering of low qual

</details>

You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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`.
You will only find the `.fastq` files in the results directory if you provide ` --save_preprocessed_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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

### Bowtie2

Expand All @@ -282,7 +282,7 @@ 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 have a `.bam` file if you specify `--save_hostremoval_bam`. This will contain _both_ mapped and unmapped reads. You will only get FASTQ files if you specify to save `--save_hostremoval_unmapped` - these contain only unmapped 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`.
By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only have a `.bam` file if you specify `--save_hostremoval_bam`. This will contain _both_ mapped and unmapped reads. You will only get FASTQ files if you specify to save `--save_hostremoval_unmapped` - these contain only unmapped 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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::info
Unmapped reads in FASTQ are only found in this directory for short-reads, for long-reads see [`samtools/fastq/`](#samtools-fastq).
Expand Down Expand Up @@ -335,7 +335,7 @@ Unlike Bowtie2, minimap2 does not produce an unmapped FASTQ file by itself. See

</details>

This directory will be present and contain the unmapped reads from the `.fastq` format from long-read minimap2 host removal, if `--save_hostremoval_unmapped` is supplied. 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`.
This directory will be present and contain the unmapped reads from the `.fastq` format from long-read minimap2 host removal, if `--save_hostremoval_unmapped` is supplied. 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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

:::info
For short-read unmapped reads, see [bowtie2](#bowtie2).
Expand All @@ -344,7 +344,7 @@ For short-read unmapped reads, see [bowtie2](#bowtie2).
### Analysis Ready Reads

:::info
This optional results directory will only be present in the pipeline results when supplying `--save_analysis_ready_reads`.
This optional results directory will only be present in the pipeline results when supplying `--save_analysis_ready_fastqs`.
:::

<details markdown="1">
Expand Down Expand Up @@ -391,7 +391,7 @@ This is the last possible preprocessing step, so if you have multiple runs or li

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.

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`.
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_fastqs`, in which case the reads will be in the folder `analysis_ready_reads`.

### Bracken

Expand Down
2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -259,7 +259,7 @@ nf-core/taxprofiler offers four main preprocessing steps for preprocessing raw s
- [**Run merging**](#run-merging): concatenation of multiple FASTQ chunks/sequencing runs/libraries of a sample.

:::info
You can save the 'final' reads used for classification/profiling from any combination of these steps with `--save_analysis_ready_reads`.
You can save the 'final' reads used for classification/profiling from any combination of these steps with `--save_analysis_ready_fastqs`.
:::

#### Read Processing
Expand Down