assembly_finder - v0.8.0

assembly_finder v0.8.0 - 24-10-2024

Simplified help output, bumped ncbi-datasets version and added option to only download summary tables.

Features

• Added option to only download summary tables by @farchaab in https://github.com/metagenlab/assembly_finder/pull/24 ## Changes
• Updated workflows and bump tool versions by @farchaab in https://github.com/metagenlab/assembly_finder/pull/23
• Simplified help output fefa3899710162b6fa77f70f6bed6c8b11e01947 b4b8fb6a6515fd6d5b224184d2a567dbff4f53d1

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.7...v0.8.0

- Python
Published by farchaab over 1 year ago

assembly_finder - v0.7.7

Summary

Small release to fix docker file, update unit tests and other small fixes

Additions

• 2621c5cd2e6f87b3f6ab3782390cec655b2020da Added unit tests for taxa and accessions string inputs
• be970e813a9022260a4ee9e41d3dd4e83b57a9cc Added ps in container (for usage in nextflow), and install curl, rsync and p7zip via apt

Changes

• 82c790406675c82135c6e53905cdc553d8a104fd Added taxon column when downloading taxa in assembly_summary.tsv
• 621e8b4ba0d2a33ef8d952ff49931b9b235cfb6e Removed curl, rsync and p7zip from env.yaml
• 066cf8a6749be42b40a35b7fabc339a75559cde3 Bumped version

Fixes

• d0fc28b6570d2b87ae456ad0e0fd0414e169e02a Return query when it does not contain GCF, GCA or "_"

PRs

• Fixed github workflows by @farchaab in https://github.com/metagenlab/assembly_finder/pull/21
• Release 0.7.7 by @farchaab in https://github.com/metagenlab/assembly_finder/pull/22

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.6...v0.7.7

- Python
Published by farchaab almost 2 years ago

assembly_finder - Release 0.7.6

Summary

Small release to fix container, conda-envs and unit-tests

Additions

71f057b835d6fe61548047b14db548af10b7c054 Added CITATION.cff file

Changes

• Conda:
  • 1896d62569fcaef09478e062f62f4d36c6f15aaf Seperated utils conda envs
  • 6d7724707ac5029f9eabe00c4d6d31451be03a28 Froze env versions
  • 4175e0ca010efdb594f7fa0f4462613164608b81 Seperated csvtk and taxonkit envs
  • a8acd3c1c6db56749461ca56457742d7e3c422ec Changed conda prefix to .snakemake/conda
  • 6fce3120f69831b3e3287a6cf28f32f18a6ce58f Use p7zip instead of unzip for extracting archive on macos
• Container:
  • 0a7e034bebe9260d6124c88ffa10551a62d34aaa Added all dependencies in env.yaml

Fixes

• d845dc2462de5f8232272c889485024309c3d497 Fixed arch64 container build
• 4bbc993588d6cc42038e7c6fc01aa991ba780b22 Fixed XDGCACHEHOME
• d3cb2a93bd4dd67bf68b010386cef9918cf8ba0c Fixed unexpected characters in query wildcard
• 9b18f69 Include genome and seq-report by default (fixes missing input files)
• 050dff4f288f0b014e269f15c3bf42c79232bdc5 Fixed macos-latest unit-test

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.5...v0.7.6

- Python
Published by farchaab almost 2 years ago

assembly_finder - Release 0.7.5

What's Changed

• Fix genomes paths performance by @farchaab in https://github.com/metagenlab/assembly_finder/pull/16

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.4...v0.7.5

- Python
Published by farchaab almost 2 years ago

assembly_finder - assembly_finder v0.7.4

Summary

Small patch to fix api-key arg

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.3...v0.7.4

- Python
Published by farchaab about 2 years ago

assembly_finder - assembly_finder v0.7.3

Summary

Small patch to download reference or representative genomes by default, and docs update

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.2...v0.7.3

- Python
Published by farchaab about 2 years ago

assembly_finder - assembly_finder v0.7.2

Summary

Small patch to fix taxonkit env and change temp directory cleanup

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.7.1...v0.7.2

- Python
Published by farchaab about 2 years ago

assembly_finder - Release 0.7.1

Summary

Release to add snaketool template and taxonkit for lineage taxonomy

What's Changed

• fb6d86132b740917315aec7806c526ca8a43caf9 Added snaketool template
• 1f5f8bde77a87471ee15431b6f4ae09a2db7e11b Added unit tests
• c551224e6e7667d3d3e1d7f37aa2d12efa8d8a4d Added taxonkit for lineage table
• b8f4b8d532e542f40118c844b73d96f52d5a1655 Cleanup for json and jsonl files
• 4704373484ccd90c2b61d931e9dc093d2ea20229 97b2b547d49616def2449bc3bb996bca5a7c3660 Added conda envs for each rule
• 8fbc583062b7f5a4ec40c99fa677b66979a3261a Updated docs

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.6.2...v0.7.1

- Python
Published by farchaab about 2 years ago

assembly_finder - assembly_finder v0.6.2

Summary

Small release to fix version and taxonomy

What's Changed

• 6fad4952e0e17a1d2ffcdd040cad33165e04e9c0 Removes floats in lineage_id, and uppercase rank
• 573e8bed48310d2a0a0c264166913e40ea4e49d8 Adds version without empty line

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.6.1...v0.6.2

- Python
Published by farchaab about 2 years ago

assembly_finder - assembly_finder v0.6.1

Summary

Small release to fix spaces in genome paths

What's Changed

• edcedad2c8f04c32672b408231365880df581646 Fixes spaces in genome paths
• 3583df172298e1d6fbb837265d21b74ac8bad915 Appends long metavars like lineage ranks to help

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.6.0...v0.6.1

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.6.0

Summary

Major release to use ncbi-datasets-cli to fetch genomes, assembly info and taxonomy

What's Changed

• Release 0.6.0 by @farchaab in https://github.com/metagenlab/assembly_finder/pull/11

Full Changelog: https://github.com/metagenlab/assembly_finder/compare/v0.4.2...v0.6.0

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.4.2

Summary

• Small release to fix genbank paths and checksum verification

Changes

• a98eacd5083c87ec501279ebb06fb61c675ea374 Changed default exclude to anomalous
• 25264d8aea11fa64cee7d009dd783f5fd46ae222 Use python os.path for rule paths
• f9307883959a6b52f9a120a20322d96218161398 Changed default outdir

Fixes

• fedcb6f859e91608907fe74d0ce2486edeb310d5 fixes absolute paths when downloading from genbank
• 25264d8aea11fa64cee7d009dd783f5fd46ae222 fixes #9

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.4.1

Summary

• Small patch to fix input table parsing ### Fixes
• 800f44b Fixed entries and nb conversion to integers

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.4.0

Summary

• Input table requires column names now
• Auto complete of missing columns when input is a table
• Added a more flexible input search (assembly accessions, names...)
• Added retries in downloads
• Bug fixes
• updated README

Additions

• e38d74e Added input table examples
• 39db04a Added auto complete of missing columns in input table
• d5575c3 Added retries in download rules

Changes

• fbe383a Improved params names
• a1d8ebb d1cacbc Changed input search to support assembly names, accessions and uid
• 3f4f6f0 Renamed extensions param to suffix
• d6a8b96 Use column names in input table
• e9d7e70 Changed params ordering
• 8ed3daa Improved click help message (click choices)
• 43bac2f Snakemake args are now added with "--" (--force intead of force for example)
• 1bfd3c7 Updated documentation in README ### Fixes
• 2f76629 Fixed index error when no fasta is downloaded
• 3f4f6f0 Fixed checksum extension bug

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.3.3

Summary

• Added option to download assembly reports, fasta and more (gff,gtf ...)
• Bug fixes ## Details ### Additions
• 306278ccff83fbd4feb83cec099c97fe040800de Added option to download assembly fasta, reports, gff, gtf... #5 ### Changes
• 75374611e07acab99b9c32568e1e211ce9d59933 Simplified params names
• f570581c75863636f4c92a8ad4b8dc91063e0d54 Removed unnecessary dictionary ### Fixes
• ab40351cba5fa1aed8af44a2c61e130772ec47ad 5c98c715d1787723a6eec98d0811f8937a1b6658 Fixed boolean params
• 9f837933b07f1de993956b59a2dd2554e71f04e9 Fixed assembly level filter #4

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.3.2

Summary

• Small update to fix the bioconda package ## Details ### Fixes
• 2ac37e012e542c19a5a3c69a49aa7c2b5f0ba26b Add Snakefile and scripts in bioconda package
• bb9a9e4e7ed1590cbbfb235f2dba88d6490646d7 Fixed empty assembly method, and sequencing technology columns from assembly report

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.3.1

assembly_finder v0.3.1

Summary

• Small update to use up-to-date aspera-cli from bioconda
  ## Details ### Changes
• e4b85d34366aadff9f38e586e423e660fbd5abee Changed path to ascp private key
• 931114fef070ad098570abbb3461c0306e048b8a Use updated aspera-cli from bioconda instead of HCC

- Python
Published by farchaab over 2 years ago

assembly_finder - assembly_finder v0.3.0

Summary of changes

• Simplified assembly_finder cli
• Added checksum verification
• Split summary table into three tables for sequence, assembly and taxonomy summary
• Allow different parameters (assembly status, refseq category ...) for each entry
• Improvements and bugfixes ## Details ### Additions
• 25e7f0598a53579fcf2bf37d0e4455540aeb37f1 81efbf6f9107a00f85f2e9585c8c544602af4e60 Added sequencing technology, organism name, Biosource submission types in assembly table
• 81efbf6f9107a00f85f2e9585c8c544602af4e60 Added sequence table to have sequence info (header to taxid correspondance)
• 81efbf6f9107a00f85f2e9585c8c544602af4e60 Added taxonomy table to have linear taxonomy info
  
• 12dfee45f8c3cc8362103b7d4563a1a82bae2b5e Allow for different assembly search parameters for each entry
• dbca07a07e45173a8530e39e4a4cd428bb28c929 Added sha256 checksum verification
• 5907660f279b3e8b3e58d400271c55a77f254a5b 56a0389f8d1189ef72c67dd5955b0737bdbf6318 Added taxa.sqlite rules and option to avoid saving it in the conda env

Changes

• 81efbf6f9107a00f85f2e9585c8c544602af4e60 Split summary table into three tables for sequence, assembly and taxonomy summary
• 12dfee45f8c3cc8362103b7d4563a1a82bae2b5e Changed sort priority to refseq category then assembly status, followed by coverage and N50
  
• a17e3a16b4235a69dcd8f6e1e53ddea0c031c8ff Improved directory structure (moved scripts to bin directory)
• cb1f4afb88e1e09783d42243ec639def7e305e2f Removed run sub-command for simpler cli
• 25e7f0598a53579fcf2bf37d0e4455540aeb37f1 Renamed summary table headers (no more CamelCase !)
• 43a8d0ea71c7d99839f35c2fa5ad1e462bd1d498 Removed required NCBI email and key
• 2335ea7389dee36fc22f2ea940dc3eaa8c6be32a Removed wget option
• 8c947f47e8586665804d7f9b898b5106294011c1 Updated dependency versions ### Fixes
• 6f43cd7218ac51c48ae7bae791d0ed6798b58a91 Fixed number of assembly selection with or without rank filtering

- Python
Published by farchaab over 2 years ago

assembly_finder -

• added wrapper
• added ntargetrank to retrieve n genomes of each target rank (e.g species) within a taxon (e.g an entire family)

- Python
Published by tpillone almost 5 years ago

assembly_finder - First alpha release

Pipeline that searches and download genomes from NCBI's assembly database.

For this release assembly_finder:

• Takes taxonomy identifiers or taxonomic ranks plus the number of assemblies to download as inputs in a tsv file.

• Outputs a summary table listing information on the downloaded assemblies.

• Has a search term that includes all assemblies except the ones from metagenomes (by default).

• Has a filtering function that prioritizes reference or representative genomes (by default).

- Python
Published by idfarbanecha almost 7 years ago