mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-21 10:48:18 +00:00
Update MALT to older version due to major bug in most recent version (#1796)
* Rollback version * Start work rollback to 0.4.1 * Further changes * Re do dynamic flag creation * Prettier.
This commit is contained in:
James A. Fellows Yates
GitHub
parent
6e7c0e945b
commit
be8d7b3293
7 changed files with 73 additions and 79 deletions
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@ -2,16 +2,17 @@ process MALT_BUILD {
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label 'process_high'
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conda (params.enable_conda ? "bioconda::malt=0.53" : null)
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conda (params.enable_conda ? "bioconda::malt=0.41" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
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'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
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'quay.io/biocontainers/malt:0.41--1' }"
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input:
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path fastas
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val seq_type
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path gff
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path map_db
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path mapping_file
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val mapping_type
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val mapping_db
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output:
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path "malt_index/" , emit: index
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@ -29,19 +30,36 @@ process MALT_BUILD {
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} else {
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avail_mem = task.memory.giga
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}
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def igff = gff ? "-igff ${gff}" : ""
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def valid_db = ['eggnog', 'interpro2go', 'kegg', 'seed', 'taxonomy']
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if ( !valid_db.contains(mapping_db) ) { error "Unrecognised mapping database value for MALT_BUILD. Options: eggnog, interpro2go, kegg, seed, taxonomy" }
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switch ( "${mapping_type}" ) {
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case "gi":
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mapping_prefix = "-g"; break
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case "ref":
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if ( mapping_db == "taxonomy" ) {
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mapping_prefix = '-a'
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} else {
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mapping_prefix = "-r"
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};break
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case "syn":
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mapping_prefix = "-s"; break
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default:
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error '[MALT_BUILD] Mapping type not recognised. Options: gi, ref, syn'; break
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}
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type_flag = mapping_prefix + '2' + mapping_db + " " + mapping_file
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"""
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malt-build \\
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-J-Xmx${avail_mem}g \\
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-v \\
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--input ${fastas.join(' ')} \\
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-s $seq_type \\
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$igff \\
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-d 'malt_index/' \\
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-t $task.cpus \\
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$args \\
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-mdb ${map_db}/*.db |&tee malt-build.log
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$type_flag |&tee malt-build.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -22,20 +22,24 @@ tools:
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input:
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- fastas:
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type: file
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description: Directory of, or FASTA reference files for indexing
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description: Directory of, or list of FASTA reference files for indexing
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pattern: "*/|*.fasta"
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- seq_type:
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type: string
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description: Type of input data
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pattern: "DNA|Protein"
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- gff:
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- mapping_file:
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type: file
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description: Directory of, or GFF3 files of input FASTA files
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pattern: "*/|*.gff|*.gff3"
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- map_db:
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type: file
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description: MEGAN .db file from https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
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pattern:
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description: An unzipped MEGAN mapping file in .abin format (pre-2020), downloadable from https://software-ab.informatik.uni-tuebingen.de/download/megan6/old.html
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pattern: "*.abin"
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- mapping_type:
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type: value
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description: What type of accession to use for database construction.
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pattern: "gi|ref|syn"
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- mapping_type:
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type: value
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description: Which database the mapping file is derived from.
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pattern: "eggnog|interpro2go|kegg|seed|taxonomy"
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output:
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- versions:
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@ -2,10 +2,10 @@ process MALT_RUN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::malt=0.53" : null)
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conda (params.enable_conda ? "bioconda::malt=0.41" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/malt:0.53--hdfd78af_0' :
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'quay.io/biocontainers/malt:0.53--hdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/malt:0.41--1' :
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'quay.io/biocontainers/malt:0.41--1' }"
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input:
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tuple val(meta), path(fastqs)
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@ -33,7 +33,6 @@ process MALT_RUN {
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"""
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malt-run \\
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-J-Xmx${avail_mem}g \\
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-t $task.cpus \\
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-v \\
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-o . \\
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@ -6,21 +6,12 @@ include { UNZIP } from '../../../../modules/unzip/main.nf'
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include { MALT_BUILD } from '../../../../modules/malt/build/main.nf'
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workflow test_malt_build {
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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seq_type = "DNA"
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gff = []
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map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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seq_type = "DNA"
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map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
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mapping_type = 'ref'
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mapping_db = 'taxonomy'
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UNZIP ( map_db )
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MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map{ it[1] } )
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}
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workflow test_malt_build_gff {
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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seq_type = "DNA"
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gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
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map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
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UNZIP ( map_db )
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MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map{ it[1] } )
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UNZIP ( map_accession )
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MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
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}
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@ -1,13 +1,16 @@
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- name: malt build
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command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build -c ./tests/config/nextflow.config -c ./tests/modules/malt/build/nextflow.config
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- name: malt build test_malt_build
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command: nextflow run ./tests/modules/malt/build -entry test_malt_build -c ./tests/config/nextflow.config -c ./tests/modules/malt/build/nextflow.config
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tags:
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- malt
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- malt/build
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files:
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- path: output/malt/malt-build.log
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contains:
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- "Peak memory"
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- path: output/malt/malt_index/index0.idx
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md5sum: 1954f2c00b418d00112829b0a6adb8ce
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- path: output/malt/malt_index/ref.db
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md5sum: 772a09aeb162515485b037604399f2bd
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md5sum: 1fb74eccd5400fb23454454da1bd4c0c
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- path: output/malt/malt_index/ref.idx
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md5sum: 7dea362b3fac8e00956a4952a3d4f474
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- path: output/malt/malt_index/ref.inf
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@ -15,34 +18,10 @@
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- path: output/malt/malt_index/table0.db
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- path: output/malt/malt_index/table0.idx
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- path: output/malt/malt_index/taxonomy.idx
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md5sum: bb335e7c378a5bd85761b6eeed16d984
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md5sum: 13aa81314892b5537319fca2a63a2c31
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- path: output/malt/malt_index/taxonomy.map
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md5sum: f6b05bbab2149e388cb769098e14d433
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md5sum: 1e972302ae6d705b8abb377cfafd380a
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- path: output/malt/malt_index/taxonomy.tre
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md5sum: bde26a1fff5c63d3046d3863607a1e70
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- name: malt build gff
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command: nextflow run ./tests/modules/malt/build_test -entry test_malt_build_gff -c ./tests/config/nextflow.config -c ./tests/modules/malt/build/nextflow.config
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tags:
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- malt
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- malt/build
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files:
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- path: output/malt/malt_index/aadd.dbx
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md5sum: 4e2ed57e713d5372bd09350f447cdf53
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- path: output/malt/malt_index/aadd.idx
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md5sum: 0994061bc8673ebd283fa6546c3dd12c
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- path: output/malt/malt_index/index0.idx
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md5sum: 1954f2c00b418d00112829b0a6adb8ce
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- path: output/malt/malt_index/ref.db
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md5sum: 772a09aeb162515485b037604399f2bd
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- path: output/malt/malt_index/ref.idx
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md5sum: 7dea362b3fac8e00956a4952a3d4f474
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- path: output/malt/malt_index/ref.inf
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md5sum: b146842067cf278ef1d23e6c2e7c0c35
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- path: output/malt/malt_index/table0.db
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- path: output/malt/malt_index/table0.idx
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- path: output/malt/malt_index/taxonomy.idx
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md5sum: bb335e7c378a5bd85761b6eeed16d984
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- path: output/malt/malt_index/taxonomy.map
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md5sum: f6b05bbab2149e388cb769098e14d433
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- path: output/malt/malt_index/taxonomy.tre
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md5sum: bde26a1fff5c63d3046d3863607a1e70
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md5sum: 79c2322475a8eebc57607ff36c1e4728
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- path: output/unzip/nucl_acc2tax-Jul2019.abin/nucl_acc2tax-Jul2019.abin
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md5sum: b2deb1df50ebcec4de71a6beec6226d7
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@ -8,18 +8,19 @@ include { MALT_RUN } from '../../../../modules/malt/run/main.nf'
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workflow test_malt_run {
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fastas = 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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seq_type = "DNA"
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map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
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fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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seq_type = "DNA"
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map_accession = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/nucl_acc2tax-Jul2019.abin.zip", checkIfExists: true) ]
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mapping_type = 'ref'
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mapping_db = 'taxonomy'
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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mode = "BlastN"
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UNZIP ( map_db )
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MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map { it[1] } )
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UNZIP ( map_accession )
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MALT_BUILD ( fastas, seq_type, UNZIP.out.unzipped_archive.map{ it[1] }, "ref", "taxonomy" )
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MALT_RUN ( input, mode, MALT_BUILD.out.index )
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}
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@ -1,8 +1,10 @@
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- name: malt run
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command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c ./tests/config/nextflow.config -c ./tests/modules/malt/run/nextflow.config
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- name: malt run test_malt_run
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command: nextflow run ./tests/modules/malt/run -entry test_malt_run -c ./tests/config/nextflow.config -c ./tests/modules/malt/run/nextflow.config
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tags:
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- malt
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- malt/run
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- malt
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files:
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- path: output/malt/test_1.rma6
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- path: output/malt/test-malt-run.log
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contains:
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- "Peak memory"
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- path: output/malt/test_1.rma6
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