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:
Michael L Heuer 2022-01-17 03:24:40 -06:00 committed by GitHub
parent 280712419d
commit c9587d76e2
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GPG key ID: 4AEE18F83AFDEB23
9 changed files with 77 additions and 23 deletions

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@ -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}":

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@ -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

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@ -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)

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@ -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)

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@ -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)

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@ -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)

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@ -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"

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@ -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 )
}

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@ -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