Parallel Accession Download

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession, and is therefore much faster and more robust to errors when many accessions need to be downloaded.

Changelog

[0.1.14] 2024-05-27

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy0

[0.1.13] 2024-04-22

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy1

[0.1.12] 2024-04-16

Changed

• Remove unnecessary param_value_from_file step and directly pass file with identifiers to fasterqdump

[0.1.11] 2024-04-08

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.10+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy0

[0.1.10] 2024-03-11

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.10+galaxy0

[0.1.9] 2023-11-27

Automatic update

• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1

[0.1.8] 2023-11-20

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1

[0.1.7] 2023-11-10

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy3 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy0

[0.1.6] 2023-09-27

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy3

[0.1.5] 2023-09-12

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy1

[0.1.4] 2023-02-17

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.5+galaxy0

[0.1.3] 2022-02-04

Automatic update

• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.11.0+galaxy1

[0.1.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.1.1] 2021-07-23

Added

Added RO-Crate metadata file. No functional changes.

[0.1] - 2021-06-23

Added

• Initial version of Parallel Accession Download workflow.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
• toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.1+galaxy0
• __APPLY_RULES__