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Remove duplicate parameters #59

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merged 2 commits into from
Dec 10, 2020
Merged

Remove duplicate parameters #59

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128c37c
Remove duplicate parameters
ewels Nov 24, 2020
f35d490
Improve error message for missing params.fasta
ewels Nov 24, 2020
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6 changes: 3 additions & 3 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -132,9 +132,9 @@ if (params.skip_mirdeep){
mature = file("$params.references_parsed/mature.fa", checkIfExists: true)
indices_mirdeep2 = Channel.fromPath("$params.references_parsed/genome.*.ebwt", checkIfExists: true).ifEmpty { exit 1, "Reference parsed genome indices not found: ${references_parsed}"}
} else {
if (params.mature) { reference_mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature file not found: ${params.mature}" }
if (params.hairpin) { reference_hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin file not found: ${params.hairpin}" }
if (params.fasta) { reference_genome = file(params.fasta, checkIfExists: true) } else { exit 1, "Reference genome file not found: ${params.fasta}" }
if (params.mature) { reference_mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature miRNA fasta file not found: ${params.mature}" }
if (params.hairpin) { reference_hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin miRNA fasta file not found: ${params.hairpin}" }
if (params.fasta) { reference_genome = file(params.fasta, checkIfExists: true) } else { exit 1, "Reference genome Fasta file not found: ${params.fasta}" }
}
}

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2 changes: 0 additions & 2 deletions nextflow.config
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Expand Up @@ -15,8 +15,6 @@ params {

// Reference genomes
genome = false
mature = false
hairpin = false
mirna_gtf = false
fasta = false
bt_index = false
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