From 901df308c893c302c186d0b003b4b431d0e3b0df Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 1 Nov 2024 11:25:16 +0000 Subject: [PATCH] [automated] Fix code linting --- CHANGELOG.md | 26 +++++++++++++------------- docs/output.md | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 24201c1..22eb9b5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 | @@ -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] diff --git a/docs/output.md b/docs/output.md index b86f5a8..1cfee72 100644 --- a/docs/output.md +++ b/docs/output.md @@ -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`. `` can be replaced by `_longReads`, `_R1` or left as `` depending on the cases mentioned in [fastp](#fastp).