mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format (#1207)
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format * fix ci failures Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
This commit is contained in:
parent
280712419d
commit
c9587d76e2
9 changed files with 77 additions and 23 deletions
|
@ -2,16 +2,16 @@ process DSHBIO_EXPORTSEGMENTS {
|
||||||
tag "${meta.id}"
|
tag "${meta.id}"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(gfa)
|
tuple val(meta), path(gfa)
|
||||||
|
|
||||||
output:
|
output:
|
||||||
tuple val(meta), path("*.fa"), emit: fasta
|
tuple val(meta), path("*.fa.gz"), emit: fasta
|
||||||
path "versions.yml" , emit: versions
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
script:
|
script:
|
||||||
|
@ -22,7 +22,7 @@ process DSHBIO_EXPORTSEGMENTS {
|
||||||
export-segments \\
|
export-segments \\
|
||||||
$args \\
|
$args \\
|
||||||
-i $gfa \\
|
-i $gfa \\
|
||||||
-o ${prefix}.fa
|
-o ${prefix}.fa.gz
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
"${task.process}":
|
"${task.process}":
|
||||||
|
|
|
@ -21,8 +21,8 @@ input:
|
||||||
e.g. [ id:'test', single_end:false ]
|
e.g. [ id:'test', single_end:false ]
|
||||||
- gfa:
|
- gfa:
|
||||||
type: file
|
type: file
|
||||||
description: Assembly segments in GFA 1.0 format
|
description: Assembly segments in uncompressed or compressed GFA 1.0 format
|
||||||
pattern: "*.{gfa}"
|
pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}"
|
||||||
output:
|
output:
|
||||||
- meta:
|
- meta:
|
||||||
type: map
|
type: map
|
||||||
|
@ -31,8 +31,8 @@ output:
|
||||||
e.g. [ id:'test', single_end:false ]
|
e.g. [ id:'test', single_end:false ]
|
||||||
- fasta:
|
- fasta:
|
||||||
type: file
|
type: file
|
||||||
description: Assembly segment sequences in FASTA format
|
description: Assembly segment sequences in gzipped FASTA format
|
||||||
pattern: "*.{fa}"
|
pattern: "*.{fa.gz}"
|
||||||
- versions:
|
- versions:
|
||||||
type: file
|
type: file
|
||||||
description: File containing software versions
|
description: File containing software versions
|
||||||
|
|
|
@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
|
||||||
tag "${meta.id}"
|
tag "${meta.id}"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(bed)
|
tuple val(meta), path(bed)
|
||||||
|
|
|
@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
|
||||||
tag "${meta.id}"
|
tag "${meta.id}"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(gff3)
|
tuple val(meta), path(gff3)
|
||||||
|
|
|
@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
|
||||||
tag "${meta.id}"
|
tag "${meta.id}"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(bed)
|
tuple val(meta), path(bed)
|
||||||
|
|
|
@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
|
||||||
tag "${meta.id}"
|
tag "${meta.id}"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.6" : null)
|
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.6--hdfd78af_0' :
|
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
|
||||||
'quay.io/biocontainers/dsh-bio:2.0.6--hdfd78af_0' }"
|
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(gff3)
|
tuple val(meta), path(gff3)
|
||||||
|
|
|
@ -82,6 +82,9 @@ params {
|
||||||
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
|
scaffolds_fasta = "${test_data_dir}/genomics/sarscov2/illumina/fasta/scaffolds.fasta"
|
||||||
|
|
||||||
assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
|
assembly_gfa = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa"
|
||||||
|
assembly_gfa_bgz = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.bgz"
|
||||||
|
assembly_gfa_gz = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.gz"
|
||||||
|
assembly_gfa_zst = "${test_data_dir}/genomics/sarscov2/illumina/gfa/assembly.gfa.zst"
|
||||||
|
|
||||||
test_single_end_bam_readlist_txt = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
|
test_single_end_bam_readlist_txt = "${test_data_dir}/genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt"
|
||||||
|
|
||||||
|
|
|
@ -11,3 +11,27 @@ workflow test_dshbio_exportsegments {
|
||||||
|
|
||||||
DSHBIO_EXPORTSEGMENTS ( input )
|
DSHBIO_EXPORTSEGMENTS ( input )
|
||||||
}
|
}
|
||||||
|
|
||||||
|
workflow test_dshbio_exportsegments_bgz {
|
||||||
|
input = [ [ id:'test_bgz' ], // meta map
|
||||||
|
[ file(params.test_data['sarscov2']['illumina']['assembly_gfa_bgz'], checkIfExists: true) ]
|
||||||
|
]
|
||||||
|
|
||||||
|
DSHBIO_EXPORTSEGMENTS ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_dshbio_exportsegments_gz {
|
||||||
|
input = [ [ id:'test_gz' ], // meta map
|
||||||
|
[ file(params.test_data['sarscov2']['illumina']['assembly_gfa_gz'], checkIfExists: true) ]
|
||||||
|
]
|
||||||
|
|
||||||
|
DSHBIO_EXPORTSEGMENTS ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
workflow test_dshbio_exportsegments_zst {
|
||||||
|
input = [ [ id:'test_zst' ], // meta map
|
||||||
|
[ file(params.test_data['sarscov2']['illumina']['assembly_gfa_zst'], checkIfExists: true) ]
|
||||||
|
]
|
||||||
|
|
||||||
|
DSHBIO_EXPORTSEGMENTS ( input )
|
||||||
|
}
|
||||||
|
|
|
@ -4,5 +4,32 @@
|
||||||
- dshbio
|
- dshbio
|
||||||
- dshbio/exportsegments
|
- dshbio/exportsegments
|
||||||
files:
|
files:
|
||||||
- path: ./output/dshbio/test.fa
|
- path: ./output/dshbio/test.fa.gz
|
||||||
md5sum: 19ed0b69970ed3fbb641c5c510ebef61
|
md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
|
||||||
|
|
||||||
|
- name: dshbio exportsegments bgz
|
||||||
|
command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_bgz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
|
||||||
|
tags:
|
||||||
|
- dshbio
|
||||||
|
- dshbio/exportsegments
|
||||||
|
files:
|
||||||
|
- path: ./output/dshbio/test_bgz.fa.gz
|
||||||
|
md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
|
||||||
|
|
||||||
|
- name: dshbio exportsegments gz
|
||||||
|
command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_gz -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
|
||||||
|
tags:
|
||||||
|
- dshbio
|
||||||
|
- dshbio/exportsegments
|
||||||
|
files:
|
||||||
|
- path: ./output/dshbio/test_gz.fa.gz
|
||||||
|
md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
|
||||||
|
|
||||||
|
- name: dshbio exportsegments zst
|
||||||
|
command: nextflow run ./tests/modules/dshbio/exportsegments -entry test_dshbio_exportsegments_zst -c ./tests/config/nextflow.config -c ./tests/modules/dshbio/exportsegments/nextflow.config
|
||||||
|
tags:
|
||||||
|
- dshbio
|
||||||
|
- dshbio/exportsegments
|
||||||
|
files:
|
||||||
|
- path: ./output/dshbio/test_zst.fa.gz
|
||||||
|
md5sum: 2b8471e1ccf84169ccb75a1c1bb9109c
|
||||||
|
|
Loading…
Reference in a new issue