nf-core_modules/tests/modules/amps/main.nf
James A. Fellows Yates e080f4c8ac
Untar unzip meta (#1408)
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNZIP as UNZIP_MALT } from '../../../modules/unzip/main.nf'
include { UNZIP as UNZIP_MALTEXTRACT } from '../../../modules/unzip/main.nf'
include { MALT_BUILD } from '../../../modules/malt/build/main.nf'
include { MALT_RUN } from '../../../modules/malt/run/main.nf'
include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
include { AMPS } from '../../../modules/amps/main.nf'
workflow test_amps {
fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
gff = []
seq_type = "DNA"
map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
mode = "BlastN"
taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
UNZIP_MALT ( map_db )
UNZIP_MALTEXTRACT ( ncbi_dir )
MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
MALT_RUN ( input, mode, MALT_BUILD.out.index )
ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
}