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Merge pull request #117 from nf-core/fix-selector-warns

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Fixes process selector warning
This commit is contained in:
James A. Fellows Yates 2022-09-04 16:23:53 +02:00 committed by GitHub
commit d093de1bd0
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5 changed files with 27 additions and 22 deletions
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6
.github/workflows/ci.yml vendored
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@ -98,5 +98,7 @@ jobs:
echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv' echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
- name: Run pipeline with test data - name: Run pipeline with test data
run: | uses: Wandalen/wretry.action@v1.0.11
nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv with:
command: nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
attempt_limit: 3

4
conf/modules.config
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@ -274,7 +274,7 @@ process {
] ]
} }
withName: 'NFCORE_TAXPROFILER:TAXPROFILER:PROFILING:MEGAN_RMA2INFO' { withName: 'MEGAN_RMA2INFO_TSV' {
ext.args = "-c2c Taxonomy" ext.args = "-c2c Taxonomy"
ext.prefix = { "${meta.id}" } ext.prefix = { "${meta.id}" }
publishDir = [ publishDir = [
@ -312,7 +312,7 @@ process {
] ]
} }
withName: 'NFCORE_TAXPROFILER:TAXPROFILER:VISUALIZATION_KRONA:MEGAN_RMA2INFO' { withName: 'MEGAN_RMA2INFO_KRONA' {
ext.args = { "--read2class Taxonomy" } ext.args = { "--read2class Taxonomy" }
ext.prefix = { "${meta.id}-${meta.db_name}" } ext.prefix = { "${meta.id}-${meta.db_name}" }
} }

5
conf/test.config
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@ -51,7 +51,10 @@ process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
} }
withName: MEGAN_RMA2INFO { withName: MEGAN_RMA2INFO_TSV {
maxForks = 1
}
withName: MEGAN_RMA2INFO_KRONA {
maxForks = 1 maxForks = 1
} }
} }

26
subworkflows/local/profiling.nf
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@ -2,16 +2,16 @@
// Run profiling // Run profiling
// //
include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main' include { MALT_RUN } from '../../modules/nf-core/modules/malt/run/main'
include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main' include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/modules/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main' include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/modules/kraken2/kraken2/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main' include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/modules/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main' include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/modules/centrifuge/kreport/main'
include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main' include { METAPHLAN3 } from '../../modules/nf-core/modules/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main' include { KAIJU_KAIJU } from '../../modules/nf-core/modules/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main' include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/modules/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main' include { DIAMOND_BLASTX } from '../../modules/nf-core/modules/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main' include { MOTUS_PROFILE } from '../../modules/nf-core/modules/motus/profile/main'
workflow PROFILING { workflow PROFILING {
take: take:
@ -109,11 +109,11 @@ workflow PROFILING {
[ meta_new, rma ] [ meta_new, rma ]
} }
MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary ) MEGAN_RMA2INFO_TSV (ch_maltrun_for_megan, params.malt_generate_megansummary )
ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log ) ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log )
ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO_TSV.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan ) ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan )
ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt ) ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO_TSV.out.txt )
} }

8
subworkflows/local/visualization_krona.nf
View file

@ -2,7 +2,7 @@
// Create Krona visualizations // Create Krona visualizations
// //
include { MEGAN_RMA2INFO } from '../../modules/nf-core/modules/megan/rma2info/main' include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_KRONA } from '../../modules/nf-core/modules/megan/rma2info/main'
include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main' include { KAIJU_KAIJU2KRONA } from '../../modules/nf-core/modules/kaiju/kaiju2krona/main'
include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main' include { KRAKENTOOLS_KREPORT2KRONA } from '../../modules/nf-core/modules/krakentools/kreport2krona/main'
include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup' include { KRONA_CLEANUP } from '../../modules/local/krona_cleanup'
@ -87,15 +87,15 @@ workflow VISUALIZATION_KRONA {
Convert MALT/MEGAN RMA2INFO files into html Krona visualisations Convert MALT/MEGAN RMA2INFO files into html Krona visualisations
*/ */
if ( params.krona_taxonomy_directory ) { if ( params.krona_taxonomy_directory ) {
MEGAN_RMA2INFO ( ch_input_classifications.malt, false ) MEGAN_RMA2INFO_KRONA ( ch_input_classifications.malt, false )
GUNZIP ( MEGAN_RMA2INFO.out.txt ) GUNZIP ( MEGAN_RMA2INFO_KRONA.out.txt )
ch_krona_taxonomy_for_input = GUNZIP.out.gunzip ch_krona_taxonomy_for_input = GUNZIP.out.gunzip
.map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]} .map{[[id: it[0]['db_name'], tool: it[0]['tool']], it[1]]}
.groupTuple() .groupTuple()
KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) ) KRONA_KTIMPORTTAXONOMY ( ch_krona_taxonomy_for_input, file(params.krona_taxonomy_directory, checkExists: true) )
ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html ) ch_krona_html.mix( KRONA_KTIMPORTTAXONOMY.out.html )
ch_versions = ch_versions.mix( MEGAN_RMA2INFO.out.versions.first() ) ch_versions = ch_versions.mix( MEGAN_RMA2INFO_KRONA.out.versions.first() )
ch_versions = ch_versions.mix( KRONA_KTIMPORTTAXONOMY.out.versions.first() ) ch_versions = ch_versions.mix( KRONA_KTIMPORTTAXONOMY.out.versions.first() )
} }