Merge pull request #135 from FertigLab/nextflow

add anndata to dgcmatrix module
FertigLab · Dec 13, 2024 · dc800bc · dc800bc
2 parents 5595e8c + 02267b6
commit dc800bc
Showing 1 changed file with 59 additions and 1 deletion.
diff --git a/nextflow/main.nf b/nextflow/main.nf
@@ -56,7 +56,7 @@ process COGAPS {
   """
 }
 
-process PREPROCESS {
+process TENX_2DGCMAT {
   tag "$meta.id"
   label 'process_low'
   container 'docker.io/satijalab/seurat:5.0.0'
@@ -98,3 +98,61 @@ process PREPROCESS {
   END_VERSIONS
   """
 }
+
+process ADATA_2DGCMAT {
+  tag "$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
+    "${task.process}":
+        hdf5r: \$(Rscript -e 'print(packageVersion("Seurat"))' | awk '{print \$2}')
+        R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
+  END_VERSIONS
+  """
+
+  script:
+  def args = task.ext.args ?: ''
+  prefix = task.ext.prefix ?: "${meta.id}"
+  """
+  mkdir "${prefix}"
+
+  Rscript -e 'message("Reading data from ", "$data");
+              f <- hdf5r::h5file(filename = "$data", mode="r");
+              i <- hdf5r::readDataSet(f[["X/indices"]]);
+              p <- hdf5r::readDataSet(f[["X/indptr"]]);
+              x <- hdf5r::readDataSet(f[["X/data"]]);
+              dims <- c(hdf5r::h5attributes(f[["X/"]])[["shape"]][1],
+                        hdf5r::h5attributes(f[["X/"]])[["shape"]][2]);
+              res <- Matrix::sparseMatrix(i = i, p = p, x = x, dims = dims, index1=FALSE);
+              message("Read matrix with dimensions: ", dims[1],",",dims[2]);
+              colnames(res) <- hdf5r::readDataSet(f[["var/_index"]]);
+              rownames(res) <- hdf5r::readDataSet(f[["obs/_index"]]);
+              hdf5r::h5close(f);
+              message("Normalizing data");
+              res <- Seurat::NormalizeData(res);
+              message("Saving");
+              saveRDS(res, file="${prefix}/dgCMatrix.rds")';
+
+  cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seurat: \$(Rscript -e 'print(packageVersion("hdf5r"))' | awk '{print \$2}')
+        Matrix: \$(Rscript -e 'print(packageVersion("Matrix"))' | awk '{print \$2}')
+        Matrix: \$(Rscript -e 'print(packageVersion("Seurat"))' | awk '{print \$2}')
+        R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
+  END_VERSIONS
+  """
+}