sra-manifest-to-concatenated-fastqs/main
Version 1

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Workflow Type: Galaxy

Tests Passing

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

SEEK ID: https://workflowhub.eu/workflows/851?version=1

Inputs

ID	Name	Description	Type
Column number with SRA ID	Column number with SRA ID	Column number in the SRA_manifest with SRA ID (usually 1)	int
Column number with final identifier	Column number with final identifier	Column number in the SRA_list with final identifier	int
SRA_manifest	SRA_manifest	Input tabular from SRA Run Selector or home made (First row needs to be a header)	File

Steps

ID	Name	Description
3	Set SRA column to 1 if at 0	toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0
4	Compute column expression	toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
5	Cut columns of interest	Cut1
6	generate table for relabelling	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1
7	Cut to get only SRA	Cut1
8	split file to get one SRA per file + header	toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
9	get Fastqs from SRA IDs	toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.1.0+galaxy1
10	relabel pair collec to get SRA+sample	__RELABEL_FROM_FILE__
11	relabel single collec to get SRA+sample	__RELABEL_FROM_FILE__
12	Apply rules	__APPLY_RULES__
13	Apply rules	__APPLY_RULES__
14	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2
15	Concatenate multiple datasets	toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets/1.4.2