feat!: Remove PREDICTHAPLO module
The developers no longer publish a single-end version of predicthaplo (see https://github.com/cbg-ethz/PredictHaplo/issues/1). Since this pipeline is targeting single-end read technologies, drop predicthaplo from the list.
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3 changed files with 0 additions and 37 deletions
6
main.nf
6
main.nf
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@ -6,7 +6,6 @@ include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/
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include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
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include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes'
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include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
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include { HAPLINK_SEQUENCES } from './modules/haplink/sequences'
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include { HAPLINK_VARIANTS } from './modules/haplink/variants'
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include { HAPLINK_VARIANTS } from './modules/haplink/variants'
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include { PREDICTHAPLO } from './modules/predicthaplo'
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include { MINIMAP2 } from './modules/minimap2'
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include { MINIMAP2 } from './modules/minimap2'
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include { NANOFILT } from './modules/nanofilt'
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include { NANOFILT } from './modules/nanofilt'
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include { QUASIRECOMB } from './modules/quasirecomb'
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include { QUASIRECOMB } from './modules/quasirecomb'
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@ -78,11 +77,6 @@ workflow {
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ch_reference
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ch_reference
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)
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)
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PREDICTHAPLO(
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ch_alignments,
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ch_reference
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)
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QUASIRECOMB( ch_alignments )
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QUASIRECOMB( ch_alignments )
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SHORAH_AMPLICON(
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SHORAH_AMPLICON(
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@ -1,27 +0,0 @@
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process PREDICTHAPLO {
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tag "${prefix}"
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label 'process_high'
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label 'predicthaplo'
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container 'quay.io/biocontainers/predicthaplo:2.1.4--h9b88814_5'
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input:
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tuple val(prefix), path(bam), path(bai)
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path(reference)
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output:
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tuple val(prefix), path("*.fa*")
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publishDir "results/${task.process}", mode: 'copy'
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when:
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task.ext.when == null || task.ext.when
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script:
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"""
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predicthaplo \\
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--sam "${bam}" \\
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--reference "${reference}" \\
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--prefix "${prefix}"
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"""
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}
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@ -19,7 +19,6 @@ params {
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// By default, run all haplotypers
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// By default, run all haplotypers
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cliquesnv = true
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cliquesnv = true
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haplink = true
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haplink = true
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predicthaplo = true
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quasirecomb = true
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quasirecomb = true
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shorah = true
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shorah = true
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viquas = true
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viquas = true
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@ -69,9 +68,6 @@ process {
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withLabel: 'haplink' {
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withLabel: 'haplink' {
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ext.when = params.haplink
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ext.when = params.haplink
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}
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}
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withLabel: 'predicthaplo' {
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ext.when = params.predicthaplo
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}
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withLabel: 'quasirecomb' {
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withLabel: 'quasirecomb' {
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ext.when = params.quasirecomb
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ext.when = params.quasirecomb
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}
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}
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