add information about tool in documentation

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)

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 |

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 |

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",