Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[Retrieve_SRR_Metadata] New wf to retrieve SRR after Terra2NCBI wf #668

Merged
merged 28 commits into from
Nov 26, 2024
Merged
Changes from 1 commit
Commits
Show all changes
28 commits
Select commit Hold shift + click to select a range
71a3ed6
inital commit part 1 retrieve srr from Biosample
fraser-combe Oct 29, 2024
fe2914a
update task and wf names and meta
fraser-combe Nov 4, 2024
47890c8
dockstore add
fraser-combe Nov 4, 2024
3f2ac27
Documentation and update column name
fraser-combe Nov 4, 2024
2bb0df4
update dockstore name
fraser-combe Nov 4, 2024
de5b45d
fraser-combe Nov 4, 2024
4eeb546
Remove unnecessary blank lines in fetch_srr_metadata WDL task
fraser-combe Nov 7, 2024
a0b9fec
Update SRR metadata workflow and documentation for clarity and accuracy
fraser-combe Nov 8, 2024
71a17fd
Remove redundant docker input from wf_update_srr_metadata workflow
fraser-combe Nov 8, 2024
2564f59
update
fraser-combe Nov 8, 2024
e99ea72
update dockstore
fraser-combe Nov 14, 2024
3ebb9fe
initial updates
fraser-combe Nov 14, 2024
8c80fec
handle multiple SRR accessionss as string version outputs
fraser-combe Nov 15, 2024
690ab6a
update task path
fraser-combe Nov 15, 2024
2799eaf
forgot to import task versioning
fraser-combe Nov 15, 2024
705c766
update dockstore yml
fraser-combe Nov 15, 2024
3ec8105
comma sep output as string instead of array
fraser-combe Nov 18, 2024
cbf6bcf
update wf name
fraser-combe Nov 18, 2024
26f5c4f
test local worked
fraser-combe Nov 18, 2024
7bcc842
set euo pipefail
fraser-combe Nov 20, 2024
988fc17
more explicit fail invalid biosample
fraser-combe Nov 21, 2024
f00cdd0
update logic failure
fraser-combe Nov 22, 2024
f9de101
logic handling valid biosample or SRA
fraser-combe Nov 22, 2024
26d8c49
enhance error handling and logging for biosample ID or SRA fetching
fraser-combe Nov 22, 2024
e186b30
Update logic for no SRR accessions and invalid samples
fraser-combe Nov 22, 2024
4995aa2
update docs version in table
fraser-combe Nov 22, 2024
e4a5bec
add sample level to docs
fraser-combe Nov 25, 2024
6cba0fc
update input and ouptut tables
fraser-combe Nov 26, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
set euo pipefail
fraser-combe committed Nov 20, 2024
commit 7bcc8428d8866568e288fc58c2fdc9737992e2a4
2 changes: 2 additions & 0 deletions tasks/utilities/data_handling/task_fetch_srr_accession.wdl
Original file line number Diff line number Diff line change
@@ -13,6 +13,8 @@ task fetch_srr_accession {
}

command <<<
set -euo pipefail

# Output the current date and fastq-dl version for debugging
date -u | tee DATE
fastq-dl --version | tee VERSION