now with conda-based images

modules/maxquant/lfq/#main.nf#

@@ -0,0 +1,34 @@
+process MAXQUANT_LFQ {
+    tag "$meta.id"
+    label 'process_long'
+
+    conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
+    } else {
+        container "wombatp/maxquant-pipeline:v0.13"
+    }
+
+    input:
+    tuple val(meta), path(fasta), path(paramfile)
+    path raw
+
+    output:
+    tuple val(meta), path("*.txt"), emit: maxquant_txt
+    path "versions.yml"          , emit: version
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
+
+    echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml
+    sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
+    sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
+    mkdir temp
+    maxquant mqpar_changed.xml
+    mv combined/txt/*.txt .
+    """
+}

modules/maxquant/lfq/Dockerfile

@@ -0,0 +1,16 @@
+FROM nfcore/base
+LABEL authors="Niclas Kildegaard Nielsen and Veit Schwämmle" \
+      description="Docker image containing all requirements for maxquant pipeline"
+
+COPY environment.yml /
+# Create the environment:
+RUN conda env create -f /environment.yml && conda clean -a
+# Make RUN commands use the new environment:
+
+# Activates the env for the program to run in
+RUN echo "source activate nf-core-maxquant" > ~/.bashrc
+ENV PATH /opt/conda/envs/nf-core-maxquant/bin:$PATH
+
+# Changes the Work dir to the SDRF file area
+WORKDIR /
+# ENTRYPOINT ["/bin/bash"]

modules/maxquant/lfq/environment.yml

@@ -0,0 +1,11 @@
+name: nf-core-maxquant
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-hexbin
+  - mono=5.14.0.177
+  - maxquant=1.6.10.43
+  - sdrf-pipelines=0.0.12
+  - bioconductor-normalyzerde=1.8

modules/maxquant/lfq/main.nf

@@ -1,12 +1,11 @@
 process MAXQUANT_LFQ {
     tag "$meta.id"
     label 'process_long'
-
-    conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
+    conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
+        container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1"
     } else {
-        container "wombatp/maxquant-pipeline:v0.13"
+        container "quay.io/biocontainers/maxquant:2.0.3.0--py310hdfd78af_1"
     }
 
     input:
@@ -22,7 +21,7 @@ process MAXQUANT_LFQ {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
+    export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:\$PATH
     cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")

tests/modules/maxquant/lfq/test.yml

@@ -7,4 +7,4 @@
     - maxquant/lfq
   files:
     - path: output/maxquant/proteinGroups.txt
-      md5sum: 02e70e7b08d8548fa64e41b0d70216bc
+      md5sum: 0d0f6aab54fe6dc717d1307bbc207324