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jannikseidel committed Nov 1, 2024
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26 changes: 13 additions & 13 deletions CHANGELOG.md
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Expand Up @@ -34,8 +34,8 @@ Added parameters:

Changed default values of parameters:

| Parameter | Old default value | New default value |
| ------------------------ | ----------------------------------------------------------------------------- | ----------------------------------------------------------------------------- |
| Parameter | Old default value | New default value |
| -------------------------- | ----------------------------------------------------------------------------- | ----------------------------------------------------------------------------- |
| `--fastp_cut_mean_quality` | 15 | 1 |
| `--kraken2db` | 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz' | 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20240605.tar.gz' |
| `--kraken2confidence` | 0.05 | 0.00 |
Expand All @@ -57,23 +57,23 @@ Changed default values of parameters:

Updated and added dependencies

| Tool | Previous version | Current version |
| Tool | Previous version | Current version |
| ------- | ---------------- | --------------- |
| bbmap | - | 39.10 |
| blastn | 2.14.1 | 2.15.0 |
| multiQC | 1.21 | 1.25.1 |
| kraken2 | 2.1.2 | 2.1.3 |
| seqkit | 2.8.0 | 2.8.2 |
| bbmap | - | 39.10 |
| blastn | 2.14.1 | 2.15.0 |
| multiQC | 1.21 | 1.25.1 |
| kraken2 | 2.1.2 | 2.1.3 |
| seqkit | 2.8.0 | 2.8.2 |

### `Deprecated`

| Parameter | New parameter | Reason |
| ------------- | ------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- |
| Parameter | New parameter | Reason |
| --------------- | --------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- |
| `--fasta` | `--fasta_blastn` | Introduction of fasta_bbduk; necessary to further distinguish the two parameters |
| `--skip_blastn` | `--validation_blastn` | blastn is now to be enabled on purpose; too resource intensive for a default setting |
| `--max_cpus` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |
| `--max_memory` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |
| `--max_time` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |
| `--max_cpus` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |
| `--max_memory` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |
| `--max_time` | - | New behavior of [nextflow](https://www.nextflow.io/docs/latest/reference/process.html#resourcelimits), `resourceLimits` can now be set via a config |

## v1.0.0 - Kobbfarbad - [2024-03-26]

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2 changes: 1 addition & 1 deletion docs/output.md
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Expand Up @@ -76,7 +76,7 @@ kraken2 classifies the reads. The important files are `*.classifiedreads.txt`, `

bbduk classifies the reads by kmer matching to a reference.
As soon as one k-mer is in the reference, the read is classified.
The important files are `*.bbduk.log` and `ids/*.bbduk.txt`.
The important files are `*.bbduk.log` and `ids/*.bbduk.txt`.
`<sample>` can be replaced by `<sample>_longReads`, `<sample>_R1` or left as `<sample>` depending on the cases mentioned in [fastp](#fastp).

<details markdown="1">
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