nf-core_modules/tests/software/nanolyse/main.nf

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add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { NANOLYSE } from '../../../software/nanolyse/main.nf' addParams( options: [suffix: '.clean'] )
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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workflow test_nanolyse {
input = [
[ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)]
]
fasta = file("https://github.com/wdecoster/nanolyse/raw/master/reference/lambda.fasta.gz", checkIfExists: true)
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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NANOLYSE ( input, fasta )
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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}