From 51e90f6145d68d7f579fb7af4ac91073765fd053 Mon Sep 17 00:00:00 2001 From: Felipe Almeida Date: Tue, 30 Apr 2024 16:40:35 -0300 Subject: [PATCH] add information about tool in documentation --- README.md | 1 + docs/index.md | 1 + docs/manual.md | 1 + nextflow_schema.json | 6 ++++++ 4 files changed, 9 insertions(+) diff --git a/README.md b/README.md index 6e512a9..d7a0034 100644 --- a/README.md +++ b/README.md @@ -222,6 +222,7 @@ In addition, users are encouraged to cite the programs used in this pipeline whe * [sra-tools](https://github.com/ncbi/sra-tools) * [Fastp](https://github.com/OpenGene/fastp) * [Porechop](https://github.com/rrwick/Porechop) +* [Porechop ABI](https://github.com/bonsai-team/Porechop_ABI) * [pycoQC](https://github.com/a-slide/pycoQC) * [bax2bam](https://anaconda.org/bioconda/bax2bam) * [bam2fastq](https://github.com/PacificBiosciences/pbtk#bam2fastx) diff --git a/docs/index.md b/docs/index.md index 480897d..b647f1f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -26,6 +26,7 @@ The pipeline wraps up the following tools and analyses: | [sra-tools](https://github.com/ncbi/sra-tools) & [entrez-direct](https://anaconda.org/bioconda/entrez-direct) | Interaction with SRA database for fetching fastqs and metadata | | [fastp](https://github.com/OpenGene/fastp) | Fast all-in-one preprocessing for FastQ files | | [porechop](https://github.com/rrwick/Porechop)** | ONT reads trimming and demultiplexing | +| [porechop ABI](https://github.com/bonsai-team/Porechop_ABI)** | *Ab initio* version of porechop | | [pycoQC](https://github.com/tleonardi/pycoQC) | ONT reads QC | | [NanoPack](https://github.com/wdecoster/nanopack) | Long reads QC and filter | | [bax2bam](https://anaconda.org/bioconda/bax2bam) | Convert PacBio bax files to bam | diff --git a/docs/manual.md b/docs/manual.md index 6f12ab7..67e8e99 100644 --- a/docs/manual.md +++ b/docs/manual.md @@ -63,6 +63,7 @@ As of version v2.5, users can also select data directly from SRA. One just need | `--lreads_min_length` | :material-close: | 500 | Length min. threshold for filtering long reads (ONT or Pacbio) | | `--lreads_min_quality` | :material-close: | 5 | Quality min. threshold for filtering long reads (ONT or Pacbio) | | `--nanopore_fastq` | :material-check: | NA | Sets path to nanopore fastq files. Pre-processes basecalled long reads | +| `--use_porechop_abi` | :material-close: | false | Tells the pipeline to use *ab initio* version of porechop. Incompatible with `--nanopore_is_barcoded`. | | `--nanopore_is_barcoded` | :material-close: | false | Tells whether your data (Nanopore or Pacbio) is barcoded or not. It will split barcodes into single files. Users with legacy pacbio data need to first produce a new barcoded_subreads.bam file | | `--nanopore_sequencing_summary` | :material-close: | NA | Path to nanopore 'sequencing_summary.txt'. Using this will make the pipeline render a sequencing statistics report using pycoQC. pycoQC reports will be saved using the files basename, so please, use meaningful basename, such as: sample1.txt, sample2.txt, etc. Preferentially, using the same basename as the fastq | | `--pacbio_bam` | :material-close: | NA | Path to Pacbio subreads.bam. Only used if user wants to basecall subreads.bam to FASTQ. Always keep subreads.bam and its relative subreads.bam.pbi files in the same directory | diff --git a/nextflow_schema.json b/nextflow_schema.json index 7e9acbf..ff2ca34 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -105,6 +105,12 @@ "fa_icon": "fas fa-filter", "default": 5 }, + "use_porechop_abi": { + "type": "boolean", + "fa_icon": "fas fa-barcode", + "description": "Do you want to use ab initio porechop implementation?", + "help_text": "Incompatible with demultiplexing." + }, "nanopore_is_barcoded": { "type": "boolean", "fa_icon": "fas fa-barcode",