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fix bug in virsorter2
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rujinlong committed Apr 13, 2023
1 parent 471c32e commit 2768259
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Showing 7 changed files with 63 additions and 22 deletions.
42 changes: 22 additions & 20 deletions .github/workflows/docker.yml
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Expand Up @@ -14,26 +14,28 @@ jobs:
fail-fast: false
matrix:
include:
- dockerfile: ./docker/viroprofiler-base/Dockerfile
image: denglab/viroprofiler-base
- dockerfile: ./docker/viroprofiler-binning/Dockerfile
image: denglab/viroprofiler-binning
- dockerfile: ./docker/viroprofiler-geneannot/Dockerfile
image: denglab/viroprofiler-geneannot
- dockerfile: ./docker/viroprofiler-host/Dockerfile
image: denglab/viroprofiler-host
- dockerfile: ./docker/viroprofiler-replicyc/Dockerfile
image: denglab/viroprofiler-replicyc
- dockerfile: ./docker/viroprofiler-taxa/Dockerfile
image: denglab/viroprofiler-taxa
- dockerfile: ./docker/viroprofiler-abundance/Dockerfile
image: denglab/viroprofiler-abundance
- dockerfile: ./docker/viroprofiler-vibrant/Dockerfile
image: denglab/viroprofiler-vibrant
- dockerfile: ./docker/viroprofiler-bracken/Dockerfile
image: denglab/viroprofiler-bracken
- dockerfile: ./docker/viroprofiler-phamb/Dockerfile
image: denglab/viroprofiler-phamb
# - dockerfile: ./docker/viroprofiler-base/Dockerfile
# image: denglab/viroprofiler-base
# - dockerfile: ./docker/viroprofiler-binning/Dockerfile
# image: denglab/viroprofiler-binning
# - dockerfile: ./docker/viroprofiler-geneannot/Dockerfile
# image: denglab/viroprofiler-geneannot
# - dockerfile: ./docker/viroprofiler-host/Dockerfile
# image: denglab/viroprofiler-host
# - dockerfile: ./docker/viroprofiler-replicyc/Dockerfile
# image: denglab/viroprofiler-replicyc
# - dockerfile: ./docker/viroprofiler-taxa/Dockerfile
# image: denglab/viroprofiler-taxa
# - dockerfile: ./docker/viroprofiler-abundance/Dockerfile
# image: denglab/viroprofiler-abundance
# - dockerfile: ./docker/viroprofiler-vibrant/Dockerfile
# image: denglab/viroprofiler-vibrant
# - dockerfile: ./docker/viroprofiler-bracken/Dockerfile
# image: denglab/viroprofiler-bracken
# - dockerfile: ./docker/viroprofiler-phamb/Dockerfile
# image: denglab/viroprofiler-phamb
- dockerfile: ./docker/viroprofiler-virsorter2/Dockerfile
image: denglab/viroprofiler-virsorter2
permissions:
contents: read
packages: write
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6 changes: 6 additions & 0 deletions README.md
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Expand Up @@ -53,6 +53,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
nextflow run deng-lab/viroprofiler -r main -profile singularity --input samplesheet.csv
```

5. Update the pipeline,

```bash
nextflow pull deng-lab/viroprofiler
```

Please refer to the [tutorial](https://deng-lab.github.io/viroprofiler/tutorial) for more information on how to run the pipeline with customized parameters and options.

## Documentation
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4 changes: 4 additions & 0 deletions conf/modules.config
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Expand Up @@ -64,6 +64,10 @@ process {
container = 'denglab/viroprofiler-taxa:v0.2'
}

withLabel: viroprofiler_virsorter2 {
container = 'denglab/viroprofiler-base:v0.1'
}

withLabel: viroprofiler_vpfkit {
container = 'denglab/viroprofiler-viewer'
}
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19 changes: 19 additions & 0 deletions docker/viroprofiler-virsorter2/Dockerfile
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@@ -0,0 +1,19 @@
FROM mambaorg/micromamba:0.25.1

LABEL author="Jinlong Ru"

USER root

# Activate conda env during docker build
ARG MAMBA_DOCKERFILE_ACTIVATE=1
# Set PATH manually, because nextflow doesn't activate base env by default.
ENV PATH=/opt/conda/bin:$PATH

# Copy conda env files
COPY ./docker/viroprofiler-virsorter2/env_*.yml /tmp

# Install packages
RUN --mount=type=cache,target=/opt/conda/pkgs micromamba install -n base -f /tmp/env_virsorter2.yml -y

# clean
RUN micromamba clean --all --yes
10 changes: 10 additions & 0 deletions docker/viroprofiler-virsorter2/env_virsorter2.yml
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@@ -0,0 +1,10 @@
name: viroprofiler-virsorter2
channels:
- conda-forge
- bioconda
dependencies:
- conda-forge::procps-ng
- virsorter=2.2.4
- seqkit
- csvtk
- conda-forge::glpk
2 changes: 1 addition & 1 deletion modules/local/setup_db.nf
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Expand Up @@ -49,7 +49,7 @@ process DB_PHAMB {


process DB_VIRSORTER2 {
label "viroprofiler_base"
label "viroprofiler_virsorter2"
label "setup"

when:
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2 changes: 1 addition & 1 deletion modules/local/viral_detection.nf
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Expand Up @@ -45,7 +45,7 @@ process CHECKV {


process VIRSORTER2 {
label "viroprofiler_base"
label "viroprofiler_virsorter2"

input:
path contigs
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