millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 08:59:55 +00:00
Code Issues Releases Packages Activity

Merge pull request #205 from genomic-medicine-sweden/optional_untar

Browse source 
Optional untar on dbs
This commit is contained in:
Sofia Stamouli 2022-12-23 13:14:04 +01:00 committed by GitHub
commit 59fd676ab3
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 7 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

10
subworkflows/local/db_check.nf
View file

@ -10,6 +10,8 @@ workflow DB_CHECK {
main:
ch_versions = Channel.empty()
ch_dbs_for_untar = Channel.empty()
ch_final_dbs = Channel.empty()
// special check to check _between_ rows, for which we must group rows together
// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
@ -37,11 +39,11 @@ workflow DB_CHECK {
skip: true
}
// TODO Filter to only run UNTAR on DBs of tools actually using?
// TODO make optional whether to save
UNTAR ( ch_dbs_for_untar.untar )
//Filter the channel to run untar on DBs of tools actually using
ch_input_untar = ch_dbs_for_untar.untar.dump()
.filter { params.run_kraken2 && it[0]['tool'] == 'kraken2' || params.run_centrifuge && it[0]['tool'] == 'centrifuge' || params.run_bracken && it[0]['tool'] == 'bracken' || params.run_kaiju && it[0]['tool'] == 'kaiju' || params.run_krakenuniq && it [0]['tool'] == 'krakenuniq' || params.run_malt && it[0]['tool'] == 'malt' || params.run_metaphlan3 && it[0]['tool'] == 'metaphlan3' }
UNTAR (ch_input_untar)
ch_versions = ch_versions.mix(UNTAR.out.versions.first())
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
emit: