fix bug in virsorter2

deng-lab · Apr 13, 2023 · 2768259 · 2768259
1 parent 471c32e
commit 2768259
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diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -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

diff --git a/README.md b/README.md
@@ -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

diff --git a/conf/modules.config b/conf/modules.config
@@ -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'
     }

diff --git a/docker/viroprofiler-virsorter2/Dockerfile b/docker/viroprofiler-virsorter2/Dockerfile
@@ -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
diff --git a/docker/viroprofiler-virsorter2/env_virsorter2.yml b/docker/viroprofiler-virsorter2/env_virsorter2.yml
@@ -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
diff --git a/modules/local/setup_db.nf b/modules/local/setup_db.nf
@@ -49,7 +49,7 @@ process DB_PHAMB {
 
 
 process DB_VIRSORTER2 {
-    label "viroprofiler_base"
+    label "viroprofiler_virsorter2"
     label "setup"
 
     when:

diff --git a/modules/local/viral_detection.nf b/modules/local/viral_detection.nf
@@ -45,7 +45,7 @@ process CHECKV {
 
 
 process VIRSORTER2 {
-    label "viroprofiler_base"
+    label "viroprofiler_virsorter2"
 
     input:
     path contigs