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Merge pull request #7 from CCBR/khmer
feat: khmer/uniquekmers module w/ stubs
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## development version | ||
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- new modules: | ||
- cutadapt | ||
- bwa/index | ||
- bwa/mem | ||
- cutadapt | ||
- khmer/uniquekmers |
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process KHMER_UNIQUEKMERS { | ||
tag "$fasta" | ||
label 'process_low' | ||
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container 'nciccbr/ccbr_khmer_3.0.0:v1' | ||
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input: | ||
path fasta | ||
val kmer_size | ||
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output: | ||
path "report.txt" , emit: report | ||
path "kmers.txt" , emit: kmers | ||
path "versions.yml", emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
def args = task.ext.args ?: '' | ||
""" | ||
unique-kmers.py \\ | ||
-k $kmer_size \\ | ||
-R report.txt \\ | ||
$args \\ | ||
$fasta | ||
grep ^number report.txt | sed 's/^.*:.[[:blank:]]//g' > kmers.txt | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' ) | ||
END_VERSIONS | ||
""" | ||
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stub: | ||
""" | ||
touch report.txt kmers.txt | ||
cat <<-END_VERSIONS > versions.yml | ||
"${task.process}": | ||
khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' ) | ||
END_VERSIONS | ||
""" | ||
} |
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name: "khmer_uniquekmers" | ||
description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more. Adapted from nf-core/modules khmer/uniquekhmers. | ||
keywords: | ||
- khmer | ||
- k-mer | ||
- effective genome size | ||
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tools: | ||
- "khmer": | ||
description: khmer k-mer counting library | ||
homepage: https://github.com/dib-lab/khmer | ||
documentation: https://khmer.readthedocs.io/en/latest/ | ||
tool_dev_url: https://github.com/dib-lab/khmer | ||
doi: "10.12688/f1000research.6924.1" | ||
licence: ["BSD License"] | ||
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input: | ||
- fasta: | ||
type: file | ||
description: fasta file | ||
pattern: "*.{fa,fasta}" | ||
- kmer_size: | ||
type: integer | ||
description: k-mer size to use | ||
pattern: "[0-9]+" | ||
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output: | ||
- report: | ||
type: file | ||
description: Text file containing unique-kmers.py execution report | ||
pattern: "report.txt" | ||
- kmers: | ||
type: file | ||
description: Text file containing number of kmers | ||
pattern: "kmers.txt" | ||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
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authors: | ||
- "@kelly-sovacool" |
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#!/usr/bin/env nextflow | ||
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nextflow.enable.dsl = 2 | ||
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include { KHMER_UNIQUEKMERS } from '../../../../../modules/CCBR/khmer/uniquekmers/main.nf' | ||
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workflow test_khmer_uniquekmers { | ||
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input = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) | ||
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KHMER_UNIQUEKMERS ( input, 50 ) | ||
} |
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process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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} |
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- name: khmer uniquekmers test_khmer_uniquekmers | ||
command: nextflow run ./tests/modules/CCBR/khmer/uniquekmers -entry test_khmer_uniquekmers -c ./tests/config/nextflow.config | ||
tags: | ||
- khmer | ||
- khmer/uniquekmers | ||
files: | ||
- path: output/khmer/kmers.txt | ||
md5sum: 496ebf23653a01c7a42d743e47c19f65 | ||
- path: output/khmer/report.txt | ||
md5sum: ee489abd3b244dea3640649e1790d55e | ||
- path: output/khmer/versions.yml |