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Merge pull request #30 from nf-core/database-untar
Adds ability to conditionally untar databases TAR files that contain DB directories
This commit is contained in:
commit
cd9e3c604c
6 changed files with 92 additions and 4 deletions
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@ -91,7 +91,7 @@ process {
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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path: { "${params.outdir}/kraken2/${meta.db_name}" },
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mode: 'copy',
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mode: 'copy',
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pattern: '.{fastq.gz,txt}'
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pattern: '*.{fastq.gz,txt}'
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]
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]
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ext.args = { "${meta.db_params}" }
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ext.args = { "${meta.db_params}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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@ -24,6 +24,8 @@
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"multiqc": {
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"multiqc": {
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
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},
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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"porechop": {
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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}
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}
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36
modules/nf-core/modules/untar/main.nf
generated
Normal file
36
modules/nf-core/modules/untar/main.nf
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@ -0,0 +1,36 @@
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process UNTAR {
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tag "$archive"
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label 'process_low'
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conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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'biocontainers/biocontainers:v1.2.0_cv1' }"
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input:
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tuple val(meta), path(archive)
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output:
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tuple val(meta), path("$untar"), emit: untar
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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untar = archive.toString() - '.tar.gz'
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"""
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tar \\
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-xzvf \\
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$args \\
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$archive \\
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$args2 \\
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
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END_VERSIONS
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"""
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}
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38
modules/nf-core/modules/untar/meta.yml
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38
modules/nf-core/modules/untar/meta.yml
generated
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@ -0,0 +1,38 @@
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name: untar
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description: Extract files.
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keywords:
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- untar
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- uncompress
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tools:
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- untar:
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description: |
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Extract tar.gz files.
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documentation: https://www.gnu.org/software/tar/manual/
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licence: ["GPL-3.0-or-later"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- archive:
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type: file
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description: File to be untar
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pattern: "*.{tar}.{gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- untar:
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type: file
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description:
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pattern: "*.*"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@joseespinosa"
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- "@drpatelh"
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@ -3,6 +3,7 @@
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//
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//
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { DATABASE_CHECK } from '../../modules/local/database_check'
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include { UNTAR } from '../../modules/nf-core/modules/untar/main'
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workflow DB_CHECK {
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workflow DB_CHECK {
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take:
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take:
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@ -17,10 +18,21 @@ workflow DB_CHECK {
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.dump(tag: "db_split_csv_out")
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.dump(tag: "db_split_csv_out")
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.map { create_db_channels(it) }
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.map { create_db_channels(it) }
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.dump(tag: "db_channel_prepped")
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.dump(tag: "db_channel_prepped")
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.set{ dbs }
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ch_dbs_for_untar = parsed_samplesheet
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.branch {
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untar: it[1].toString().endsWith(".tar.gz")
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skip: true
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}
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// TODO Filter to only run UNTAR on DBs of tools actually using?
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// TODO make optional whether to save
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UNTAR ( ch_dbs_for_untar.untar )
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ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
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emit:
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emit:
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dbs // channel: [ val(meta), [ db ] ]
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dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
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versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
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versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
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}
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}
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@ -42,7 +42,7 @@ workflow INPUT_CHECK {
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}
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}
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
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def create_fastq_channel(LinkedHashMap row) {
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def create_fastq_channels(LinkedHashMap row) {
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// create meta map
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// create meta map
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def meta = [:]
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def meta = [:]
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meta.id = row.sample
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meta.id = row.sample
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