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fix: Specify skip params in param checks #35

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Apr 9, 2024
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fix: Specify skip params in param checks #35

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5 changes: 3 additions & 2 deletions workflows/euryale.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,9 @@ def multiqc_report = []

workflow EURYALE {
if (params.reference_fasta == null && params.diamond_db == null && params.skip_alignment == false) { exit 1, 'A reference fasta (--reference_fasta) or a DIAMOND db (--diamond_db) must be specified' }
if (params.run_kaiju == true && params.kaiju_db == null) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
if (params.run_kraken2 == true && params.kraken2_db == null) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
if (params.run_kaiju == true && params.kaiju_db == null && params.skip_classification == false) {exit 1, 'A Kaiju tar.gz database must be specified with --kaiju_db'}
if (params.run_kraken2 == true && params.kraken2_db == null && params.skip_classification == false) {exit 1, 'A Kraken2 database must be specified with --kraken2_db'}
if (params.id_mapping == null && params.skip_functional == false) {exit 1, 'An ID mapping file is necessary if you want to run functional annotation'}
if (params.host_fasta == null && params.bowtie2_db == null && params.skip_host_removal == false) {exit 1, 'Either a host reference FASTA (--host_fasta) or a pre-built bowtie2 index (--bowtie2_db) must be specified'}

ch_versions = Channel.empty()
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