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

Initialise args for umitools extract #502

Merged
merged 3 commits into from
Nov 23, 2020
Merged

Initialise args for umitools extract #502

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
906d610
Initialise args for umitools extract
drpatelh Nov 19, 2020
d563fa3
Merge branch 'dev' of https://github.com/nf-core/rnaseq into dsl2
drpatelh Nov 23, 2020
a84b4c8
Change genome wording
drpatelh Nov 23, 2020
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
1 change: 1 addition & 0 deletions conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ params {
publish_files = ['txt':'', 'html':'fastqc', 'zip':'fastqc']
}
'umitools_extract' {
args = ""
publish_files = ['log':'']
}
'sortmerna' {
Expand Down
2 changes: 1 addition & 1 deletion rnaseq.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ params.summary_params = [:]
*/
// Check if genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
exit 1, "Genome '${params.genome}' was not found in any config files made available to the pipeline. Currently, the available genomes are ${params.genomes.keySet().join(", ")}"
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This was reported in nf-core/atacseq#126 but fixing here because it will eventually be propagated to the pipeline template and then out to each of these pipelines when the DSL2 pipeline template is eventually released.

}

// Auto-load genome files from genome config
Expand Down