move consensus to seqera containers

CHANGELOG.md

@@ -64,6 +64,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Updated test configurations and `.nftignore` files
 - Improved subworkflow organization and consistency (typos, remove unused code blocks, spacing, comments, readability)
 - Massive speed up to run_consensus.R
+- Migrated consensus module from custom Docker container to Seqera Wave containers
 
 ### `Removed`
 

modules/local/consensus/environment.yml

@@ -0,0 +1,10 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::bioconductor-complexheatmap=2.26.1
+  - bioconda::bioconductor-rtracklayer=1.70.1
+  - conda-forge::r-data.table=1.17.8
+  - conda-forge::r-dplyr=1.2.1
+  - conda-forge::r-ggpubr=0.6.3
+  - conda-forge::r-ggrepel=0.9.8

modules/local/consensus/main.nf

@@ -1,34 +1,36 @@
 process RUN_CONSENSUS {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
-    conda "bioconda::bioconductor-rtracklayer bioconda::bioconductor-complexheatmap conda-forge::r-ggrepel conda-forge::r-data.table conda-forge::r-dplyr conda-forge::r-ggpubr "
-    container 'nf-core/rnadnavar_renv_consensus:1.0'
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/ed/ed5e97c2fc53fb46675998f4f5472807f217043994cd4f490b0eb8887c31ceed/data'
+        : 'community.wave.seqera.io/library/bioconductor-complexheatmap_bioconductor-rtracklayer_r-data.table_r-dplyr_pruned:b2d4632cc9bf5c6e'}"
 
     input:
-        tuple val(meta), path(input_file, stageAs: "inputs/*"), val(caller)
+    tuple val(meta), path(input_file, stageAs: "inputs/*"), val(caller)
 
     output:
-        tuple val(meta), path('*.consensus.vcf')                , optional:true , emit: vcf
-        tuple val(meta), path('*.consensus_*.vcf'), val(caller) , optional:true , emit: vcf_separate
-        tuple val(meta), path('*.consensus.maf')                , optional:true , emit: maf
-        tuple val(meta), path('*.consensus_*.maf'), val(caller) , optional:true , emit: maf_separate
-        path("*.pdf")                                           , optional:true , emit: pdf
-        path "versions.yml"                                                     , emit: versions
+    tuple val(meta), path('*.consensus.vcf'), optional: true, emit: vcf
+    tuple val(meta), path('*.consensus_*.vcf'), val(caller), optional: true, emit: vcf_separate
+    tuple val(meta), path('*.consensus.maf'), optional: true, emit: maf
+    tuple val(meta), path('*.consensus_*.maf'), val(caller), optional: true, emit: maf_separate
+    path ("*.pdf"), optional: true, emit: pdf
+    path "versions.yml", emit: versions
 
     when:
-        task.ext.when == null || task.ext.when
+    task.ext.when == null || task.ext.when
 
     script:
-        def args = task.ext.args ?: ''
-        def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
 
-        """
-        run_consensus.R --input_dir=inputs/ --out_prefix=${prefix}.consensus --cpu=$task.cpus $args
+    """
+    run_consensus.R --input_dir=inputs/ --out_prefix=${prefix}.consensus --cpu=${task.cpus} ${args}
 
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            R: \$(echo \$(R --version 2>&1) | head -n 1)
-        END_VERSIONS
-        """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        R: \$(echo \$(R --version 2>&1) | head -n 1)
+    END_VERSIONS
+    """
 }

modules/local/maf_filtering/environment.yml

@@ -2,6 +2,5 @@ name: maf_filtering
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::pandas=1.4.3
+  - conda-forge::pandas=1.4.3