{"repo":"nf-core/bamtofastq","free":true,"listed":false,"github":"https://github.com/nf-core/bamtofastq","clone":"git clone https://github.com/nf-core/bamtofastq.git","description":"Converts bam or cram files to fastq format and does quality control.","language":"Nextflow","stars":32,"topics":["nextflow","nf-core","pipeline","workflow","bamtofastq","cramtofastq","conversion"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/bamtofastq is a bioinformatics best-practice analysis pipeline that converts (un)mapped .bam or .cram files into fq.gz files. Initially, it auto-detects, whether the input file contains single-end or paired-end reads. Following this step, the reads are sorted using samtools collate and extracted with samtools fastq . Furthermore, for mapped bam/cram files it is possible to only convert reads mapping to a specific region or chromosome. The obtained FastQ files can then be used to further process with other pipelines. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtai","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/bamtofastq/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}