wf-fastq.md

Uploading FastQ sequencing read data to ENA using ENAdumper

Prerequisites

1. Register a Webin account at ENA for submitting files
2. Register a study at ENA and get a study ID
3. Register your samples to acquire the sample sheet from ENA
4. The sample sheet will act as a key-file linking the sample names to the corresponding ENA sample IDs. Example below:

TYPE	ACCESSION	ALIAS
SAMPLE	ERS00000001	S1
SAMPLE	ERS00000002	S2
SAMPLE	ERS00000003	S3
SAMPLE	ERS00000004	S4
SAMPLE	ERS00000005	S5
SAMPLE	ERS00000006	S6

Running the ENAdumper workflow

1. The workflow assumes that the FastQ datasets have already been compressed to save storage space
2. The main input is a tsv file containing the paths and sample names of the compressed FastQ files. Example below:

FILEPATH	ALIAS
/path/to/reads/S1.fastq.gz	S1
/path/to/reads/S2.fastq.gz
/path/to/reads/S3.fastq.gz
/path/to/reads/S4.fastq.gz	S4
/path/to/reads/S5.fastq.gz
/path/to/reads/S6.fastq.gz	S6

3. If the sample name is not provided, the basename of the read file will be used instead.
4. Example command for uploading FastQ data with ENAdumper:
   ENAdumper --fastq_list list.tsv --key sample_sheet.tsv --study PRJEB00001 -n BATCH1 -user Webin-0001 -pass Banana1
5. ENAdumper will upload FastQ files in parallel, which can be set using the --processes option
6. After upload is complete, a template spreadsheet will be generated that can be submitted to include the files in the permanent archive
7. It is highly recommended to double-check the template spreadsheet before submitting it to ENA