fastq-dl - v3.0.1

3.0.1

Changed

• require Python >=3.9 and <3.13 (3.13 compatibility will come in a future release)

- Python
Published by rpetit3 12 months ago

fastq-dl - v3.0.0

3.0.0

Added

• --ignore to ignore MD5 checksums

Changed

• (BREAKING) the --force flag now overwrites existing files, but will check the MD5 checksums of the downloaded files. Previously, it would force download the file, but ignore the MD5 as well. See https://github.com/rpetit3/fastq-dl/issues/21#issuecomment-2190686184 for more details. Use the newly added --ignore flag to ignore MD5 checksums too.
• require Python >=3.9
• updated depends and poetry lock file
• began reorganizing code for better maintainability

- Python
Published by rpetit3 over 1 year ago

fastq-dl - v2.0.4

2.0.4

Fixed

• mismatch in --version output

- Python
Published by rpetit3 over 2 years ago

fastq-dl - v2.0.3

2.0.3

Added

• Explicit setting of SRA Lite or SRA Normalized (default) downloads
• --sra-lite to prefer SRA Lite downloads from SRA
• print usage on empty options

- Python
Published by rpetit3 over 2 years ago

fastq-dl - v2.0.2

2.0.2

Added

• --only-download-metadata to skip FASTQ downloads, and retrieve only the associated metadata @alienzj
• fallback on SRA for metadata retrieval @gtonkinhill
• include prefetchfor SRA downloads @gtonkinhill
• added --force to overwrite existing downloads @gtonkinhill
• update github actions

- Python
Published by rpetit3 over 2 years ago

fastq-dl - v2.0.1

2.0.1

Fixed

• Invalid fieldName(s) in ENA query @mbhall88
• gitpod dependency and setup
• dependabot PR

- Python
Published by rpetit3 almost 3 years ago

fastq-dl - v2.0.0

2.0.0

Added

• Shorthand option -m for --max-attempts and -v for --verbose
• If metadata is unavailable from ENA, try fetching metadata from SRA using pysradb
• Provided query is validated against accession regular expressions
• Support for Biosample/Sample accessions
• Rich click, logging support, type hints
• Support for Gitpod
• Query must now be passed as --accession/-a
• Packaging with poetry
• README improvements

Removed

• Deprecated --sra_only parameter is now removed
• --ftp_only no longer required without Aspera support
• Non-functioning --debug option
• Uneeded logging levels

- Python
Published by rpetit3 about 3 years ago

fastq-dl - v1.2.0

• remove support for Aspera
• remove manual vdb-config (no longer required in sra-tools>=3.0.1)
• use accession in pigz command

- Python
Published by rpetit3 about 3 years ago

fastq-dl - v1.1.1

Handle experiment accessions with duplicate run accessions

Example: https://www.ebi.ac.uk/ena/browser/view/ERX012546?show=reads

- Python
Published by rpetit3 over 3 years ago

fastq-dl - v1.1.0

Big thanks to @mbhall88 for submitting https://github.com/rpetit3/fastq-dl/pull/5 with the following improvements!

Added

• -o shorthand option for --outdir
• a flag -F/--only-provider, which supercedes --sra_only. I left --sra_only in there for backwards compatibility and added a deprecation notice in the help description for it.
• Conda environment file
• Dockerfile. Feel free to try out an image from my quay.io repo here.

Changed

• Move everything into a main function to avoid variable shadowing
• Provider is now optional and defaults to ena. I've also made the option case insensitive, rather than listing the cased versions of the available providers
• If ENA download fails, try SRA
• Reduced a bunch of execute calls which were mostly operations easily dealt with by pathlib.Path
• Changed md5sum to use hashlib.md5 instead of executing a subprocess call to md5sum
• Moved a bunch of import statements out of function bodies to the top of the file

Removed

• Docstring at top of file as this is a mirror of argparse's help menu and creates needless maintenance

- Python
Published by rpetit3 almost 4 years ago

fastq-dl - Explicit use of ftp for ENA downloads

Includes fix for https://github.com/rpetit3/fastq-dl/issues/3 which requires "ftp://" be added to the beginning of URL for ENA downloads.

- Python
Published by rpetit3 about 5 years ago

fastq-dl - Workaround for SRA Toolkit interactive requirements

- Python
Published by rpetit3 over 5 years ago

fastq-dl - Update ENA API end points

- Python
Published by rpetit3 over 5 years ago

fastq-dl - Failure to copy, paste and update

Fixed issue when merging runs. I failed to update the syntax for executor usage

- Python
Published by rpetit3 over 6 years ago

fastq-dl - Try SRA, Try ENA

This release adds a fallback onto ENA, when a FASTQ may not have been indexed onto SRA yet. In other words the FASTQ exists on ENA but not SRA.

- Python
Published by rpetit3 over 6 years ago

fastq-dl - Quick fix for ENA downloads

A few things were left out in the port from ena-dl. fixed a few syntax bugs as well

- Python
Published by rpetit3 over 6 years ago

fastq-dl - A wild fastq-dl v1.0.0 has appeared!

This is the initial release of fastq-dl.

- Python
Published by rpetit3 over 6 years ago