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feat: include metaphlan3 in workflow

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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
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14
workflows/taxprofiler.nf
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@ -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 { CAT_FASTQ } from '../modules/nf-core/modules/cat/fastq/main'
include { MALT_RUN } from '../modules/nf-core/modules/malt/run/main' include { MALT_RUN } from '../modules/nf-core/modules/malt/run/main'
include { KRAKEN2_KRAKEN2 } from '../modules/nf-core/modules/kraken2/kraken2/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 { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2' kraken2: it[2]['tool'] == 'kraken2'
metaphlan3: it[2]['tool'] == 'metaphlan3'
unknown: true unknown: true
} }
@ -163,6 +164,13 @@ workflow TAXPROFILER {
db: it[3] 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 MODULE: RUN PROFILING
*/ */
@ -174,6 +182,10 @@ workflow TAXPROFILER {
KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db ) 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 MODULE: MultiQC
*/ */