Merge pull request #128 from FertigLab/126-nextflow-module

126 nextflow module

nextflow/main.nf

@@ -53,3 +53,46 @@ process COGAPS {
   END_VERSIONS
   """
 }
+
+process PREPROCESS {
+  tag "$meta.id"
+  label 'process_low'
+  container 'docker.io/satijalab/seurat:5.0.0'
+
+  input:
+      tuple val(meta), path(data) 
+  output:
+      tuple val(meta), path("${prefix}/dgCMatrix.rds"), emit: dgCMatrix
+      path "versions.yml"                             , emit: versions
+
+  stub:
+  def args = task.ext.args ?: ''
+  prefix = task.ext.prefix ?: "${meta.id}"
+
+  """
+  mkdir "${prefix}"
+  touch "${prefix}/dgCMatrix.rds"
+  cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seurat: \$(Rscript -e 'print(packageVersion("Seurat"))' | awk '{print \$2}')
+        R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
+  END_VERSIONS
+  """
+
+  script:
+  def args = task.ext.args ?: ''
+  prefix = task.ext.prefix ?: "${meta.id}"
+  """
+  mkdir "${prefix}"
+
+  Rscript -e 'res <- Seurat::Read10X("$data/raw_feature_bc_matrix/");
+              res <- Seurat::NormalizeData(res);
+              saveRDS(res, file="${prefix}/dgCMatrix.rds")';
+
+  cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seurat: \$(Rscript -e 'print(packageVersion("Seurat"))' | awk '{print \$2}')
+        R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
+  END_VERSIONS
+  """
+}