github.com/aofarrel/SRANWRP/pull_FASTQs_from_SRA_by_run

# SRAnwrp [](https://hub.docker.com/r/ashedpotatoes/sranwrp/tags) SRAnwrp ("Saran Wrap") envelops several SRA-related tools in the warm, polyethylene embrace of a single Ubuntu-based Docker image and some optional assorted workflows. For the sake of simplicity, releases on main follow the same versioning scheme as the Docker image. ## What tasks can it perform? The combination of e-direct and sra-tools allows it do basically anything you can do from SRA's website. These exist in the form of WDL workflows -- [more on WDL here](./wdl.md). ### Pulling FASTQs * [Pull paired FASTQs from a list of run accessions (SRR/ERR/DRR)](./workflows/pull_paired_FASTQ_by_run_accession.wdl) * [Pull paired FASTQs from a lit of BioSample accessions - can be SRS or SAME notation](./workflows/pull_paired_FASTQ_by_biosample.wdl) * Plus some bonus [non-workflow pulling tasks](./tasks/pull_fastqs.wdl) * *Note* -- as a pre-3.0.5 version of fasterq-dump is being used, pulling non-Illumina fastqs is not supported. * *Note* -- it is recommended you set the disk_size variable to 20x the size of the largest .sra that you want to download. ### Getting Organism + TaxID from a list of BioProject/BioSample accessions There's a lot of BioProjects on SRA, and some of them are multi-species. Use [this workflow](./workflows/get_organisms_from_bioproject.wdl) to get a list of all run accessions, and said run accessions' species and TaxIDs, from a list of BioProject accessions. If you instead have a list of BioSamples, use [this workflow](./workflows/get_organisms_from_biosample.wdl) to get species and taxid (as well as a list of all run accessions). ### Getting sample accessions from run accessions (SRR/ERR/DRR) If you have a list of run accessions, [this workflow](./workflows/get_samples_from_runs.wdl) will get a list of sample accessions that they cover. Some samples have more than one run -- those samples will only appear in the output once. ### Other stuff? Here's [some other tasks](./tasks/processing_tasks.wdl) that can help you convert between data types. ## What's included in the Docker image? Non-exhaustive list: * The TB reference genome and a BED of its commonly masked regions * bash-5.1.16(1)-release * [bedtools-latest](https://github.com/arq5x/bedtools2) * [bc-latest](https://www.gnu.org/software/bc/) * bcftools-1.16 * cpan-latest * curl-latest * [entrez-direct-latest](https://www.ncbi.nlm.nih.gov/books/NBK179288/) (aka edirect) * gcc-latest * git-latest * htslib-1.16 * make-latest * Matplotlib-latest * [numpy-latest](https://github.com/numpy/numpy) * [pandas-latest](https://github.com/pandas-dev/pandas) * [pigz-latest](https://github.com/madler/pigz) * python-3.12 * **note:** must be called with `python3` instead of `python` (and `pip3` instead of `pip`) when running non-interactively * [samtools-1.16](https://github.com/samtools/samtools) * mpileup, minimap2, fixmate, etc * [seqtk-latest](https://github.com/lh3/seqtk) * [sra-tools-3.0.1](https://github.com/ncbi/sra-tools) (aka SRAtools, SRA tools, SRA toolkit, etc) * align-info, fastq-dump, fasterq-dump, prefetch, sam-dump, sra-pileup, etc * fyi: [ncbi/ncbi-vdb](https://github.com/ncbi/ncbi-vdb) was merged with sra-tools in sra-tools-3.0.0 and vdb-get was retired in 3.0.1 * sudo-latest * [taxoniumtools-latest](https://github.com/theosanderson/taxonium/tree/master/taxoniumtools) * tree-latest * vim-latest * wget-latest ## Who builds? Right now, the image is built and pushed manually. You'll need to include your own copy of the TB reference tarball -- it can be created with clockwork refprep, or downloaded from [this Google bucket](https://console.cloud.google.com/storage/browser/_details/topmed_workflow_testing/tb/ref/index_H37Rv_reference_output/Ref.H37Rv.tar). MD5s are provided in this repo as a double-check. ## Why? * Docker Hub's latest version of staphb/sratoolkit, as of my writing this in October 2022, [runs version 2.9.2 (see command 15)](https://hub.docker.com/layers/staphb/sratoolkit/latest/images/sha256-84fc990e6d04f263d7bea82dcbff7f5dd9182ab5234314bb0daf2e2db977e4a0?context=explore), which [doesn't work at all anymore](https://github.com/ncbi/sra-tools/issues/714) * Existing Docker images tend to contain either the SRA toolkit or Entrez Direct, not both * Building SRA Toolkit on your own, without conda, is not intuitive * Building SRA Toolkit on your own, with conda, is also not intutive (you usually end up with v2.10 which only sometimes works) * No need to run `vdb-config --interactive` or any other interactive process before using anything in this image; SRA Toolkit's config file is generated while building the image