diff --git a/conf/modules.config b/conf/modules.config index 9e334bc..620ae1d 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -82,7 +82,7 @@ process { publishDir = [ path: { "${params.outdir}/kraken2/${meta.db_name}" }, mode: 'copy', - pattern: '.{fastq.gz,txt}' + pattern: '*.{fastq.gz,txt}' ] ext.args = { "${meta.db_params}" } ext.when = params.run_kraken2 diff --git a/modules.json b/modules.json index 9a7f1df..96a43d8 100644 --- a/modules.json +++ b/modules.json @@ -25,7 +25,7 @@ "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41" }, "untar": { - "git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a" + "git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918" } } } diff --git a/modules/nf-core/modules/untar/main.nf b/modules/nf-core/modules/untar/main.nf index bbae948..dc43fb7 100644 --- a/modules/nf-core/modules/untar/main.nf +++ b/modules/nf-core/modules/untar/main.nf @@ -8,19 +8,19 @@ process UNTAR { 'biocontainers/biocontainers:v1.2.0_cv1' }" input: - path archive + tuple val(meta), path(archive) output: - path "$untar" , emit: untar - path "versions.yml", emit: versions + tuple val(meta), path("$untar"), emit: untar + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - untar = archive.toString() - '.tar.gz' + untar = archive.toString() - '.tar.gz' """ tar \\ -xzvf \\ diff --git a/modules/nf-core/modules/untar/meta.yml b/modules/nf-core/modules/untar/meta.yml index e877a97..d426919 100644 --- a/modules/nf-core/modules/untar/meta.yml +++ b/modules/nf-core/modules/untar/meta.yml @@ -10,11 +10,21 @@ tools: documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - archive: type: file description: File to be untar pattern: "*.{tar}.{gz}" output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - untar: type: file description: diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf index 6f061d7..641108d 100644 --- a/subworkflows/local/db_check.nf +++ b/subworkflows/local/db_check.nf @@ -3,6 +3,7 @@ // include { DATABASE_CHECK } from '../../modules/local/database_check' +include { UNTAR } from '../../modules/nf-core/modules/untar/main' workflow DB_CHECK { take: @@ -17,19 +18,19 @@ workflow DB_CHECK { .dump(tag: "db_split_csv_out") .map { create_db_channels(it) } .dump(tag: "db_channel_prepped") - .set{ dbs } - parsed_samplesheet .branch { - untar: it[0]['db_path'].toString().endsWith(".tar.gz") + untar: it[1].toString().endsWith(".tar.gz") skip: true } .set{ ch_dbs_for_untar } + // TODO Filter to only run UNTAR on DBs of tools actually using? + // TODO make optional whether to save UNTAR ( ch_dbs_for_untar.untar ) - ch_final_dbs = ch_dbs_for_untar.skip.mix( ch_dbs_untarred ) + ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar ) emit: dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]