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added singularity; edge NXF version

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This commit is contained in:
kevinmenden 2020-12-17 07:33:44 +01:00
parent f35850bf14
commit d75cb75111
6 changed files with 37 additions and 11 deletions
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10
.github/workflows/bowtie_align.yml vendored
View file

@ -16,16 +16,20 @@ on:
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2

11
.github/workflows/bowtie_index.yml vendored
View file

@ -14,16 +14,21 @@ on:
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Python
uses: actions/setup-python@v2

8
software/bowtie/align/main.nf
View file

@ -11,8 +11,12 @@ process BOWTIE_ALIGN {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
} else {
container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0"
}
input:
tuple val(meta), path(reads)

5
software/bowtie/align/meta.yml
View file

@ -29,6 +29,11 @@ params:
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
- save_unaligned:
type: boolean
description: Save unaligned reads

9
software/bowtie/index/main.nf
View file

@ -11,9 +11,12 @@ process BOWTIE_INDEX {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1"
} else {
container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1"
}
input:
path fasta

5
software/bowtie/index/meta.yml
View file

@ -29,6 +29,11 @@ params:
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- fasta:
type: file