1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-10 23:03:10 +00:00

Start getting database prep ready

This commit is contained in:
James Fellows Yates 2022-03-21 15:07:59 +01:00
parent 9fac82d342
commit c7f022008c
5 changed files with 81 additions and 2 deletions

View file

@ -23,6 +23,9 @@
},
"multiqc": {
"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
},
"untar": {
"git_sha": "7ec09d0ef4df89617baacc9b2dafcddb7cd4b05a"
}
}
}

36
modules/nf-core/modules/untar/main.nf generated Normal file
View file

@ -0,0 +1,36 @@
process UNTAR {
tag "$archive"
label 'process_low'
conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
input:
path archive
output:
path "$untar" , emit: untar
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
untar = archive.toString() - '.tar.gz'
"""
tar \\
-xzvf \\
$args \\
$archive \\
$args2 \\
cat <<-END_VERSIONS > versions.yml
"${task.process}":
untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
}

28
modules/nf-core/modules/untar/meta.yml generated Normal file
View file

@ -0,0 +1,28 @@
name: untar
description: Extract files.
keywords:
- untar
- uncompress
tools:
- untar:
description: |
Extract tar.gz files.
documentation: https://www.gnu.org/software/tar/manual/
licence: ["GPL-3.0-or-later"]
input:
- archive:
type: file
description: File to be untar
pattern: "*.{tar}.{gz}"
output:
- untar:
type: file
description:
pattern: "*.*"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@joseespinosa"
- "@drpatelh"

View file

@ -19,8 +19,20 @@ workflow DB_CHECK {
.dump(tag: "db_channel_prepped")
.set{ dbs }
parsed_samplesheet
.branch {
untar: it[0]['db_path'].toString().endsWith(".tar.gz")
skip: true
}
.set{ ch_dbs_for_untar }
UNTAR ( ch_dbs_for_untar.untar )
ch_final_dbs = ch_dbs_for_untar.skip.mix( ch_dbs_untarred )
emit:
dbs // channel: [ val(meta), [ db ] ]
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ]
}

View file

@ -35,7 +35,7 @@ workflow INPUT_CHECK {
}
// Function to get list of [ meta, [ fastq_1, fastq_2 ] ]
def create_fastq_channel(LinkedHashMap row) {
def create_fastq_channels(LinkedHashMap row) {
// create meta map
def meta = [:]
meta.id = row.sample