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Remove params call in ivar variants module (#1203)
* Remove params call in ivar variants module * Update main.nf
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3 changed files with 31 additions and 27 deletions
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@ -11,6 +11,7 @@ process IVAR_VARIANTS {
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tuple val(meta), path(bam)
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path fasta
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path gff
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val save_mpileup
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output:
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tuple val(meta), path("*.tsv") , emit: tsv
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@ -21,14 +22,14 @@ process IVAR_VARIANTS {
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
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def features = params.gff ? "-g $gff" : ""
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def features = gff ? "-g $gff" : ""
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def mpileup = save_mpileup ? "tee ${prefix}.mpileup |" : ""
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"""
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samtools mpileup \\
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$args2 \\
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--reference $fasta \\
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$bam | \\
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$save_mpileup \\
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$mpileup \\
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ivar variants \\
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$args \\
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$features \\
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@ -29,6 +29,9 @@ input:
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type: file
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description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.
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patter: "*.gff"
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- save_mpileup:
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type: boolean
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description: Save mpileup file generated by ivar variants
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output:
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- meta:
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type: map
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@ -5,40 +5,40 @@ nextflow.enable.dsl = 2
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include { IVAR_VARIANTS } from '../../../../modules/ivar/variants/main.nf'
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workflow test_ivar_variants_no_gff_no_mpileup {
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params.gff = false
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params.save_mpileup = false
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input = [ [ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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dummy = file("dummy_file.txt")
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IVAR_VARIANTS ( input, fasta, dummy )
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gff = []
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save_mpileup = false
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IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
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}
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workflow test_ivar_variants_no_gff_with_mpileup {
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params.gff = false
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params.save_mpileup = true
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input = [ [ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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dummy = file("dummy_file.txt")
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gff = []
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save_mpileup = true
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IVAR_VARIANTS ( input, fasta, dummy )
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IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
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}
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workflow test_ivar_variants_with_gff_with_mpileup {
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params.gff = true
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params.save_mpileup = true
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input = [ [ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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input = [
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[ id:'test'],
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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IVAR_VARIANTS ( input, fasta, gff )
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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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save_mpileup = true
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IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
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}
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