{"id":47790883,"url":"https://github.com/oicr-gsi/bcl2fastq","last_synced_at":"2026-04-03T15:37:45.000Z","repository":{"id":34730771,"uuid":"38708812","full_name":"oicr-gsi/bcl2fastq","owner":"oicr-gsi","description":"Workflow for Illumina's bcl2fastq","archived":false,"fork":false,"pushed_at":"2025-09-10T19:33:51.000Z","size":4660,"stargazers_count":1,"open_issues_count":2,"forks_count":2,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-09-10T23:35:42.110Z","etag":null,"topics":["base-calling","bcl2fastq","illumina","workflow"],"latest_commit_sha":null,"homepage":"","language":"C++","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/oicr-gsi.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2015-07-07T19:04:55.000Z","updated_at":"2025-07-02T18:42:15.000Z","dependencies_parsed_at":"2025-04-25T18:24:21.309Z","dependency_job_id":"66706550-5740-4aa0-8e1e-e9343ea7966a","html_url":"https://github.com/oicr-gsi/bcl2fastq","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/oicr-gsi/bcl2fastq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fbcl2fastq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fbcl2fastq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fbcl2fastq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fbcl2fastq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/oicr-gsi","download_url":"https://codeload.github.com/oicr-gsi/bcl2fastq/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oicr-gsi%2Fbcl2fastq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31360807,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-03T15:19:21.178Z","status":"ssl_error","status_checked_at":"2026-04-03T15:19:20.670Z","response_time":107,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["base-calling","bcl2fastq","illumina","workflow"],"created_at":"2026-04-03T15:37:43.617Z","updated_at":"2026-04-03T15:37:44.979Z","avatar_url":"https://github.com/oicr-gsi.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# bcl2fastq\n\nThe workflow wraps around Illumina's bcl2fastq software which demultiplexes sequencing data and converts base call (BCL) files into FASTQ files. For every cycle of a sequencing run, the Real-Time Analysis software generates a BCL file containing base calls and associated quality scores (Q-scores). This is the root workflow as the most NGS applications require FASTQ inputs.\n\n## Overview\n\n## Dependencies\n\n* [bcl2fastq](https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)\n\n\n## Usage\n\n### Cromwell\n```\njava -jar cromwell.jar run bcl2fastq.wdl --inputs inputs.json\n```\n\n### Inputs\n\n#### Required workflow parameters:\nParameter|Value|Description\n---|---|---\n`lanes`|Array[Int]+|The lane numbers to process from this run\n`mismatches`|Int|Number of mismatches to allow in the barcodes (usually, 1)\n`modules`|String|The modules to load when running the workflow. This should include bcl2fastq and the helper scripts.\n`samples`|Array[Sample]+|The information about the samples. Tname of the sample which will determine the output file prefix. The list of barcodes in the format i7-i5 for this sample. If multiple barcodes are provided, they will be merged into a single output.\n`runDirectory`|String|{'description': \"The path to the instrument's output directory.\", 'vidarr_type': 'directory'}\n\n\n#### Optional workflow parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`basesMask`|String?|None|An Illumina bases mask string to use. If absent, the one written by the instrument will be used.\n`timeout`|Int|40|The maximum number of hours this workflow can run for.\n\n\n#### Optional task parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`process.bcl2fastq`|String|\"bcl2fastq\"|The name or path of the BCL2FASTQ executable.\n`process.bcl2fastqJail`|String|\"bcl2fastq-jail\"|The name ro path of the BCL2FASTQ wrapper script executable.\n`process.extraOptions`|String|\"\"|Any other options that will be passed directly to bcl2fastq.\n`process.ignoreMissingBcls`|Boolean|false|Flag passed to bcl2fastq, allows missing bcl files.\n`process.ignoreMissingFilter`|Boolean|false|Flag passed to bcl2fastq, allows missing or corrupt filter files.\n`process.ignoreMissingPositions`|Boolean|false|Flag passed to bcl2fastq, allows missing or corrupt positions files.\n`process.memory`|Int|32|The memory for the BCL2FASTQ process in GB.\n`process.temporaryDirectory`|String|\".\"|A directory where bcl2fastq can dump massive amounts of garbage while running.\n`process.threads`|Int|8|The number of processing threads to use when running BCL2FASTQ\n\n\n### Outputs\n\nOutput | Type | Description | Labels\n---|---|---|---\n`fastqs`|Array[Output]+|A list of FASTQs generated and annotations that should be applied to them.|\n\n\n## Commands\n \n This section lists command(s) run by bcl2fastq workflow\n \n * Running bcl2fastq\n \n Convert basecalls to fastq\n \n ```\n     BCL2FASTQ_JAIL \n       -t TMP_DIR \n       -s SAMPLES_JSON \n       -- BCL2FASTQ \n       --barcode-mismatches MISMATCHES \n       --input-dir INPUT_DIR \n       --intensities-dir RUN_DIR/Data/Intensities \n       --no-lane-splitting \n       --processing-threads THREADS \n       --runfolder-dir RUN_DIR \n       --tiles TITLES \n       --interop-dir TMP_DIR \n       \n       Optional Parameters:\n \n       --ignore-missing-bcls \n       --ignore-missing-filter \n       --ignore-missing-positions\n       --use-bases-mask CUSTOM_BASE_MASK \n         EXTRA_OPTIONS\n ```\n ## Support\n\nFor support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to gsi@oicr.on.ca .\n\n_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Fbcl2fastq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Foicr-gsi%2Fbcl2fastq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Fbcl2fastq/lists"}