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

make gubbins flexible #23

Merged
merged 3 commits into from
Dec 5, 2024
Merged

make gubbins flexible #23

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
ec5e4f0
make gubbins flexible
taranewman Dec 5, 2024
81d5d00
put only gubbins in if statement
taranewman Dec 5, 2024
1ff7f24
update comment
taranewman Dec 5, 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
16 changes: 9 additions & 7 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,16 +65,18 @@ workflow {
// The basic idea is to build up a channel with the following structure:
// [provenance_file_1.yml, provenance_file_2.yml, provenance_file_3.yml...]]
// ...and then concatenate them all together in the 'collect_provenance' process.
ch_pipeline_prov = pipeline_provenance.out
ch_snippy_prov = snippy_core.out.provenance
ch_gubbins_prov = gubbins.out.provenance
ch_snp_sites_prov = snp_sites.out.provenance
ch_iqtree_prov = iqtree.out.provenance
ch_shiptv_prov = shiptv.out.provenance

// Now, combine these channels in the desired order
ch_pipeline_prov = pipeline_provenance.out
ch_snippy_prov = snippy_core.out.provenance
ch_snp_sites_prov = snp_sites.out.provenance
ch_iqtree_prov = iqtree.out.provenance
ch_shiptv_prov = shiptv.out.provenance

// Add gubbins output if applicable and combine these channels in the desired order

if (!params.skip_gubbins) {
ch_gubbins_prov = gubbins.out.provenance

ch_provenance = ch_pipeline_prov
.concat(ch_snippy_prov)
.concat(ch_gubbins_prov)
Expand Down