millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-09-21 06:42:04 +00:00
Code Issues Releases Packages Activity

feat: include metaphlan3 in workflow

Browse source
This commit is contained in:
Moritz E. Beber 2022-03-18 16:01:33 +01:00
parent 4d2960c06f
commit 69db920610
1 changed files with 13 additions and 1 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

14
workflows/taxprofiler.nf
View file

@ -60,7 +60,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/
include { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
include { MALT_RUN } from '../modules/nf-core/modules/malt/run/main'
include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/main'
include { METAPHLAN3 } from '../modules/nf-core/modules/metaphlan3/main'
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@ -130,6 +130,7 @@ workflow TAXPROFILER {
.branch {
malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2'
metaphlan3: it[2]['tool'] == 'metaphlan3'
unknown: true
}
@ -163,6 +164,13 @@ workflow TAXPROFILER {
db: it[3]
}
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
/*
MODULE: RUN PROFILING
*/
@ -174,6 +182,10 @@ workflow TAXPROFILER {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db )
}
if ( params.run_metaphlan3 ) {
METAPHLAN3 ( ch_input_for_metaphlan3.reads, ch_input_for_metaphlan3.db )
}
/*
MODULE: MultiQC
*/