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Code Issues Releases Packages Activity

Add run_krona option to allow skipping Krona chart creation

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This commit is contained in:
Thomas A. Christensen II 2022-06-27 08:41:42 -05:00
parent 15ac8b39fa
commit 18284e6e32
Signed by: millironx
GPG key ID: 139C07724802BC5D
5 changed files with 12 additions and 2 deletions
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1
conf/test.config
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@ -37,6 +37,7 @@ params {
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_krona = true
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true

1
conf/test_nopreprocessing.config
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@ -37,6 +37,7 @@ params {
run_metaphlan3 = true
run_centrifuge = true
run_diamond = true
run_krona = true
}
process {

3
nextflow.config
View file

@ -125,6 +125,9 @@ params {
run_diamond = false
diamond_output_format = 'tsv' // TSV is only format with taxonomic information apparently
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated!
// krona
run_krona = false
}
// Load base.config by default for all pipelines

3
nextflow_schema.json
View file

@ -433,6 +433,9 @@
},
"diamond_save_reads": {
"type": "boolean"
},
"run_krona": {
"type": "boolean"
}
}
}

6
workflows/taxprofiler.nf
View file

@ -213,8 +213,10 @@ workflow TAXPROFILER {
/*
SUBWORKFLOW: VISUALIZATION_KRONA
*/
VISUALIZATION_KRONA ( PROFILING.out.profiles )
ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
if ( params.run_krona ) {
VISUALIZATION_KRONA ( PROFILING.out.profiles )
ch_versions = ch_versions.mix( VISUALIZATION_KRONA.out.versions )
}
/*
MODULE: MultiQC