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.

Sign up for GitHub

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

Jump to bottom

Re-add AdapterRemovalFixPrefix once conda build updated/fixed #587

Closed
jfy133 opened this issue Oct 21, 2020 · 1 comment
Closed

Re-add AdapterRemovalFixPrefix once conda build updated/fixed #587

jfy133 opened this issue Oct 21, 2020 · 1 comment
Assignees
@jfy133
Labels
bug Something isn't working enhancement New feature or request
Milestone
2.4 "Wangen"

Comments

@jfy133
Copy link
Member

jfy133 commented Oct 21, 2020

For people who still want to run dedup
@jfy133 jfy133 added this to the V2.3 "Wangen" milestone Oct 21, 2020
@jfy133 jfy133 added bug Something isn't working enhancement New feature or request labels Oct 21, 2020
@jfy133
Copy link
Member Author

jfy133 commented Oct 21, 2020

Work around:

Run with nf-core/eager with --mergedonly for AdapteRemoval to export only mapped reads, and then for dedup treat all as merged (--dedup_all_merged). This will then run without the need for the prefixes, and but also use the only type of data one should use with DeDup

@apeltzer apeltzer modified the milestones: V2.3 "Wangen", 2.2.1 Oct 23, 2020
@apeltzer apeltzer modified the milestones: 2.2.1, 2.3 "Wangen" Nov 3, 2020
@jfy133 jfy133 self-assigned this Nov 6, 2020
@jfy133 jfy133 closed this as completed Nov 10, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@jfy133 jfy133

Labels
bug Something isn't working enhancement New feature or request
Projects
None yet
Milestone
2.4 "Wangen"
Development

No branches or pull requests
2 participants
@apeltzer @jfy133