{"id":25597147,"url":"https://github.com/tleonardi/nanocompore_pipeline","last_synced_at":"2025-10-04T09:43:27.794Z","repository":{"id":49494581,"uuid":"161347010","full_name":"tleonardi/nanocompore_pipeline","owner":"tleonardi","description":"Nextflow pipeline for nanocompore analysis","archived":false,"fork":false,"pushed_at":"2023-01-12T14:31:17.000Z","size":80168,"stargazers_count":9,"open_issues_count":5,"forks_count":11,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-09-04T05:53:14.525Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HCL","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/tleonardi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-12-11T14:33:51.000Z","updated_at":"2025-06-26T20:01:59.000Z","dependencies_parsed_at":"2023-02-09T12:15:43.721Z","dependency_job_id":null,"html_url":"https://github.com/tleonardi/nanocompore_pipeline","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/tleonardi/nanocompore_pipeline","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tleonardi%2Fnanocompore_pipeline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tleonardi%2Fnanocompore_pipeline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tleonardi%2Fnanocompore_pipeline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tleonardi%2Fnanocompore_pipeline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/tleonardi","download_url":"https://codeload.github.com/tleonardi/nanocompore_pipeline/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/tleonardi%2Fnanocompore_pipeline/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278295845,"owners_count":25963427,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-04T02:00:05.491Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-02-21T12:47:54.776Z","updated_at":"2025-10-04T09:43:27.768Z","avatar_url":"https://github.com/tleonardi.png","language":"HCL","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Nanocompore pipeline\nThis repo contains the code for running the [Nanocompore](https://github.com/tleonardi/nancompore) analysis workflow using [Nextflow](https://www.nextflow.io/).\n\n## Pipeline steps\nThe pipeline runs the following steps:\n\n* Basecalls the raw fast5 files using Guppy\n* Run [pycoQC](https://github.com/a-slide/pycoQC) on Guppy's output\n* (Optionally) Prepare a fasta file for the reference transcriptome from the genome fasta and transcriptome annotation in GTF\n* Map the basecalled data to the reference using [minimap2](https://github.com/lh3/minimap2)\n* Realign the raw signal-level data to the kmers of the reference with [f5c](https://github.com/hasindu2008/f5c)\n* Collapse Nanopolish output by kmer using Nanocompore's eventalign_collapse\n* Run Nanocompore\n\nAll steps are executed in a Docker/Singularity containers.\n\n## How to run\n\n### Sample annotation\nPrepare a tab-separated file that describes the samples:\n```\nSampleName  Condition DataPath\nWT1         WT        /path/to/fast5dir\nWT2         WT        /path/to/fast5dir\nKD1         KD        /path/to/fast5dir\nKD2         KD        /path/to/fast5dir\n```\n\n### Configure the pipeline\nConfigure the pipeline by editing the _nextflow.config_ file.\n\nAll parameters are described in the comments and should be self explanatory.\n\nThe only two options that deserve an explanation are `target_trancripts` and `input_is_basecalled`.\nThe former allows you to provide the path to a text file that lists Ensembl transcript IDs of interest. \nAny transcript not present in this list will be discarded from the reference.\n`input_is_basecalled` allows you to start the pipeline __after__ the Albacore step. In order for this to work,\nthe paths in the sample annotation file must point to basecalled fast5 files.\n\n### Run the pipeline\nTo run the pipeline just execute:\n`nextflow run pipeline.nf`\n\n### Profiles\nThe pipeline is shipped with 3 profiles: local (default), lsf and aws_batch, which respectively run the processing on the local\nmachine, an LSF cluster or an AWS Batch computer environment.\nThe local profile limits the number of cuncurrent tasks to 10, which is reduced to 2 and 3 for Guppy and f5c respectively.\nThe LSF profile if configured to use dynamic memory management.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftleonardi%2Fnanocompore_pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftleonardi%2Fnanocompore_pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftleonardi%2Fnanocompore_pipeline/lists"}