diff --git a/.editorconfig b/.editorconfig
old mode 100644
new mode 100755
diff --git a/.gitattributes b/.gitattributes
old mode 100644
new mode 100755
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
old mode 100644
new mode 100755
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
old mode 100644
new mode 100755
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
old mode 100644
new mode 100755
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
old mode 100644
new mode 100755
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
old mode 100644
new mode 100755
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
old mode 100644
new mode 100755
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
old mode 100644
new mode 100755
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
old mode 100644
new mode 100755
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
old mode 100644
new mode 100755
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
old mode 100644
new mode 100755
index 5ba6b78..9d0eff7
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -41,9 +41,9 @@ jobs:
 
       - name: Build new docker image
         if: ${{ github.event.workflow_run.conclusion == 'thiswillnevertrigger' }}
-        run: docker build --no-cache . -t almurphy/scfdev:dev
+        run: docker build --no-cache . -t nfancy/scflow:dev
       - name: Pull docker image
         if: ${{ github.event.workflow_run.conclusion == 'thiswillnevertrigger' }}
         run: |
-          docker pull almurphy/scfdev:dev
-          docker tag almurphy/scfdev:dev almurphy/scfdev:dev
+          docker pull nfancy/scflow:dev
+          docker tag nfancy/scflow:dev nfancy/scflow:dev
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
old mode 100644
new mode 100755
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
old mode 100644
new mode 100755
diff --git a/.gitignore b/.gitignore
old mode 100644
new mode 100755
diff --git a/.markdownlint.yml b/.markdownlint.yml
old mode 100644
new mode 100755
diff --git a/.nf-core.yml b/.nf-core.yml
old mode 100644
new mode 100755
index 17acfd2..e0bcd34
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -9,7 +9,7 @@ lint:
 
   schema_params:
     - input
-
 actions_awsfulltest: False
 pipeline_todos: False
 actions_ci: False
+repository_type: pipeline
diff --git a/CHANGELOG.md b/CHANGELOG.md
old mode 100644
new mode 100755
diff --git a/CITATIONS.md b/CITATIONS.md
old mode 100644
new mode 100755
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
old mode 100644
new mode 100755
diff --git a/LICENSE b/LICENSE
old mode 100644
new mode 100755
diff --git a/README.md b/README.md
old mode 100644
new mode 100755
index f469759..3fe16e5
--- a/README.md
+++ b/README.md
@@ -59,7 +59,7 @@ Try the pipeline on an in-built, minimal test dataset (all inputs will be automa
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/scflow -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
+    nextflow run combiz/nf-core-scflow -r dev-nf -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
     > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
@@ -75,7 +75,7 @@ A complete, automated, scalable, and reproducible case-control analysis can then
 1. Start running your own analysis!
 
     ```bash
-    nextflow run nf-core/scflow \
+    nextflow run combiz/nf-core-scflow -r dev-nf \
     --manifest Manifest.tsv \
     --input Samplesheet.tsv \
     -c scflow_params.config \
diff --git a/assets/NO_FILE.tsv b/assets/NO_FILE.tsv
old mode 100644
new mode 100755
diff --git a/assets/email_template.html b/assets/email_template.html
old mode 100644
new mode 100755
diff --git a/assets/email_template.txt b/assets/email_template.txt
old mode 100644
new mode 100755
diff --git a/assets/nf-core-scflow_logo.png b/assets/nf-core-scflow_logo.png
old mode 100644
new mode 100755
diff --git a/assets/schema_input.json b/assets/schema_input.json
old mode 100644
new mode 100755
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
old mode 100644
new mode 100755
diff --git a/bin/scflow_annotate_integrated.R b/bin/scflow_annotate_integrated.R
deleted file mode 100755
index 4e823a6..0000000
--- a/bin/scflow_annotate_integrated.R
+++ /dev/null
@@ -1,85 +0,0 @@
-#!/usr/bin/env Rscript
-#' Annotate integrated, dims reduced and clustered sce object
-# Mahdi Moradi Marjaneh
-
-# ____________________________________________________________________________
-# Initialization ####
-
-options(mc.cores = future::availableCores())
-
-## ............................................................................
-## Load packages ####
-library(argparse)
-library(scFlow)
-
-## ............................................................................
-## Parse command-line arguments ####
-
-# create parser object
-parser <- ArgumentParser()
-
-# specify options
-required <- parser$add_argument_group("Required", "required arguments")
-optional <- parser$add_argument_group("Optional", "required arguments")
-
-required$add_argument(
-  "--sce_path",
-  help = "-path to the SingleCellExperiment",
-  metavar = "dir",
-  required = TRUE
-)
-
-required$add_argument(
-  "--categorical_covariates",
-  help = "-categorical covariates",
-  metavar = "individual,diagnosis,region,sex",
-  required = TRUE
-)
-
-### . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..
-### Pre-process args ####
-
-args <- parser$parse_args()
-args <- purrr::map(args, function(x) {
-if (length(x) == 1) {
-if (toupper(x) == "TRUE") {
-return(TRUE)
-}
-if (toupper(x) == "FALSE") {
-return(FALSE)
-}
-if (toupper(x) == "NULL") {
-return(NULL)
-}
-}
-return(x)
-})
-
-## ............................................................................
-## Annotate integrated sce ####
-
-sce <- read_sce(args$sce_path)
-
-sce <- annotate_integrated_sce(
-sce,
-categorical_covariates = args$categorical_covariates
-)
-
-dir.create(file.path(getwd(), "integration_report"))
-
-report_integrated_sce(
-  sce = sce,
-  report_folder_path = file.path(getwd(), "integration_report"),
-  report_file = "integrate_reduceDims_cluster_report_scflow",
-)
-
-print("Annotation complete, saving outputs..")
-
-## ............................................................................
-## Save Outputs ####
-
-# Save SingleCellExperiment
-write_sce(
-sce = sce,
-folder_path = file.path(getwd(), "integrated_sce")
-)
diff --git a/bin/scflow_dge.r b/bin/scflow_dge.r
index d419394..6118a21 100755
--- a/bin/scflow_dge.r
+++ b/bin/scflow_dge.r
@@ -131,7 +131,7 @@ required$add_argument(
 )
 
 required$add_argument(
-  "--fc_threshold",
+  "--logFC_threshold",
   type = "double",
   default = 1.1,
   metavar = "number",
@@ -139,7 +139,7 @@ required$add_argument(
 )
 
 required$add_argument(
-  "--pval_cutoff",
+  "--padj_cutoff",
   type = "double",
   default = 0.05,
   metavar = "number",
@@ -254,8 +254,6 @@ de_results <- perform_de(
   ref_class = args$ref_class,
   confounding_vars = args$confounding_vars,
   random_effects_var = args$random_effects_var,
-  fc_threshold = args$fc_threshold,
-  pval_cutoff = args$pval_cutoff,
   mast_method = args$mast_method,
   force_run = args$force_run,
   ensembl_mapping_file = args$ensembl_mappings,
@@ -278,8 +276,8 @@ for (result in names(de_results)) {
     )
 
     report_de(de_results[[result]],
-      fc_threshold = args$fc_threshold,
-      pval_cutoff = args$pval_cutoff,
+      logFC_threshold = args$logFC_threshold,
+      padj_cutoff = args$padj_cutoff,
       n_label = args$n_label,
       report_folder_path = file.path(getwd()),
       report_file = paste0(file_name, result, "_scflow_de_report")
@@ -289,8 +287,8 @@ for (result in names(de_results)) {
 
     p <- scFlow::volcano_plot(
       dt = de_results[[result]],
-      fc_threshold = args$fc_threshold,
-      pval_cutoff = args$pval_cutoff,
+      logFC_threshold = args$logFC_threshold,
+      padj_cutoff = args$padj_cutoff,
       n_label = args$n_label
     )
 
diff --git a/bin/scflow_dirichlet.r b/bin/scflow_dirichlet.r
index ed0bdee..1791cf7 100755
--- a/bin/scflow_dirichlet.r
+++ b/bin/scflow_dirichlet.r
@@ -65,11 +65,28 @@ required$add_argument(
   required = TRUE
 )
 
+required$add_argument(
+  "--confounding_vars",
+  help = "confounding variables",
+  metavar = "sex",
+  required = TRUE
+)
+
 # get command line options, if help option encountered print help and exit,
 # otherwise if options not found on command line then set defaults
 args <- parser$parse_args()
-args$var_order <- strsplit(args$var_order, ",")[[1]]
-if (tolower(args$var_order) == "null") { args$var_order <- NULL }
+
+if (tolower(args$var_order) == "null") { 
+  args$var_order <- NULL 
+  } else {
+    args$var_order <- strsplit(args$var_order, ",")[[1]]
+  }
+
+if (tolower(args$confounding_vars) == "null") { 
+  args$confounding_vars <- NULL 
+  } else {
+    args$confounding_vars <- strsplit(args$confounding_vars, ",")[[1]]
+  }
 
 #   ____________________________________________________________________________
 #   Start                                                                   ####
@@ -82,7 +99,8 @@ results <- model_celltype_freqs(
   celltype_var = args$celltype_var,
   dependent_var = args$dependent_var,
   ref_class = args$ref_class,
-  var_order = args$var_order
+  var_order = args$var_order,
+  confounding_vars = args$confounding_vars
 )
 
 ## ............................................................................
diff --git a/bin/scflow_ipa.r b/bin/scflow_ipa.r
index 5e09573..b4de18d 100755
--- a/bin/scflow_ipa.r
+++ b/bin/scflow_ipa.r
@@ -64,15 +64,15 @@ required$add_argument(
 )
 
 required$add_argument(
-  "--fc_threshold",
+  "--logFC_threshold",
   type = "double",
-  default = 1.1,
+  default = 0.5,
   metavar = "number",
   help = "Absolute fold-change cutoff for DE [default %(default)s]"
 )
 
 required$add_argument(
-  "--pval_cutoff",
+  "--padj_cutoff",
   type = "double",
   default = 0.05,
   metavar = "number",
@@ -121,8 +121,8 @@ for (gene_file in args$gene_file) {
 
   dt <- dt %>%
     dplyr::filter(
-      padj <= args$pval_cutoff,
-      abs(logFC) >= log2(args$fc_threshold)
+      padj <= args$padj_cutoff,
+      abs(logFC) >= args$logFC_threshold
     )
 
   if (nrow(dt) < 5) {
@@ -134,11 +134,32 @@ for (gene_file in args$gene_file) {
       organism = getOption("scflow_species"),
       enrichment_tool = args$enrichment_tool,
       enrichment_method = args$enrichment_method,
-      enrichment_database = args$enrichment_database,
-      is_output = TRUE,
-      output_dir = output_dir
+      enrichment_database = args$enrichment_database
     )
 
+    for(i in names(enrichment_result)){
+
+      output_dir_path <- paste(output_dir, i, sep = "/")
+      dir.create(output_dir_path)
+
+      res <- enrichment_result[[i]]
+
+      lapply(
+          setdiff(names(res), c("plot", "metadata")),
+          function(dt) {
+            write.table(res[dt],
+                        file = paste(output_dir_path, "/", dt, ".tsv", sep = ""),
+                        row.names = FALSE,
+                        col.names = gsub(dt, "", colnames(res[[dt]])), sep = "\t")})
+        lapply(
+          names(res$plot),
+          function(p) {
+            ggplot2::ggsave(paste(output_dir_path, "/", p, ".png", sep = ""),
+                            res$plot[[p]],
+                            device = "png", height = 8,
+                            width = 10, units = "in", dpi = 300)})
+    }
+
     if (all(unlist(lapply(
       enrichment_result, function(dt) {
         isFALSE(dt$metadata$result)
diff --git a/bin/scflow_map_celltypes.r b/bin/scflow_map_celltypes.r
index 5c913dd..7ec9204 100755
--- a/bin/scflow_map_celltypes.r
+++ b/bin/scflow_map_celltypes.r
@@ -53,6 +53,15 @@ required$add_argument(
   required = TRUE
 )
 
+required$add_argument(
+  "--annotation_level",
+  default = 1,
+  type = "integer",
+  help = "the annotation level of the reference ctd",
+  required = TRUE,
+  metavar = "N"
+)
+
 required$add_argument(
   "--species",
   help = "the biological species (e.g. mouse, human)",
@@ -101,6 +110,7 @@ sce <- map_celltypes_sce(
   ctd_folder = args$ctd_folder,
   clusters_colname = args$clusters_colname,
   cells_to_sample = args$cells_to_sample,
+  annotation_level = as.numeric(args$annotation_level),
   species = args$species
 )
 
diff --git a/bin/scflow_reduce_dims.r b/bin/scflow_reduce_dims.r
index 3ed29ae..2788e95 100755
--- a/bin/scflow_reduce_dims.r
+++ b/bin/scflow_reduce_dims.r
@@ -313,6 +313,7 @@ args <- purrr::map(args, function(x) {
 
 sce <- read_sce(args$sce_path, read_metadata = TRUE)
 
+set.seed(42)
 sce <- reduce_dims_sce(
   sce,
   input_reduced_dim = args$input_reduced_dim,
diff --git a/conf/base.config b/conf/base.config
old mode 100644
new mode 100755
index 3b0559d..2f7100d
--- a/conf/base.config
+++ b/conf/base.config
@@ -40,7 +40,7 @@ process {
         time   = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
-        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        cpus   = { check_max( 8    * task.attempt, 'cpus'    ) }
         memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
@@ -48,7 +48,9 @@ process {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
+        cpus   = { check_max( 8    * task.attempt, 'cpus'    ) }
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 8.h  * task.attempt, 'time'    ) }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
diff --git a/conf/gcp.config b/conf/gcp.config
old mode 100644
new mode 100755
diff --git a/conf/igenomes.config b/conf/igenomes.config
old mode 100644
new mode 100755
diff --git a/conf/modules.config b/conf/modules.config
old mode 100644
new mode 100755
diff --git a/conf/scflow_analysis.config b/conf/scflow_analysis.config
old mode 100644
new mode 100755
index 3af4bdd..74f1e40
--- a/conf/scflow_analysis.config
+++ b/conf/scflow_analysis.config
@@ -73,7 +73,7 @@ params {
     // Options: Dimensionality Reduction
     reddim_input_reduced_dim         = 'PCA,Liger' // *
     reddim_reduction_methods         = 'tSNE,UMAP,UMAP3D' // *
-    reddim_vars_to_regress_out       = 'nCount_RNA,pc_mito' // *
+    reddim_vars_to_regress_out       = 'total_counts,pc_mito' // *
     // umap
     reddim_umap_pca_dims             = 30
     reddim_umap_n_neighbors          = 35
@@ -115,6 +115,7 @@ params {
     // Options: Celltype Annotation
     cta_clusters_colname             = 'clusters'
     cta_cells_to_sample              = 10000
+    cta_annotation_level	     = 2
 
     // Options: Celltype Metrics Report
     cta_unique_id_var                = 'manifest'
@@ -137,8 +138,8 @@ params {
     dge_ref_class                    = 'Control'
     dge_confounding_vars             = 'cngeneson' // *
     dge_random_effects_var           = 'null'
-    dge_fc_threshold                 = 1.1
-    dge_pval_cutoff                  = 0.05
+    dge_logFC_threshold              = 0.25
+    dge_padj_cutoff                  = 0.05
     dge_n_label                      = 5
     dge_force_run                    = 'false'
     dge_max_cores                    = 'null'
@@ -153,7 +154,8 @@ params {
     dirich_celltype_var              = 'cluster_celltype'
     dirich_dependent_var             = 'diagnosis'
     dirich_ref_class                 = 'Control'
-    dirich_var_order                 = 'null' // *
+    dirich_var_order                 = 'Control,Case' // *
+    dirich_confounding_vars          = 'null' // *		
 
     // Options: Plots (Reduced Dim)
     plotreddim_reduction_methods     = 'UMAP_Liger' // *
diff --git a/conf/test.config b/conf/test.config
old mode 100644
new mode 100755
index 945ee35..8e9a385
--- a/conf/test.config
+++ b/conf/test.config
@@ -20,8 +20,8 @@ params {
 
   input = "https://raw.githubusercontent.com/nf-core/test-datasets/scflow/refs/SampleSheet.tsv"
   manifest = "https://raw.githubusercontent.com/nf-core/test-datasets/scflow/refs/Manifest.txt"
-  ensembl_mappings = "https://raw.githubusercontent.com/nfancy/test-datasets/scflow/assets/ensembl_mappings.tsv"
-  ctd_path = "https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zip"
+  ensembl_mappings = "https://raw.githubusercontent.com/nf-core/test-datasets/scflow/assets/ensembl_mappings.tsv"
+  ctd_path = "https://raw.githubusercontent.com/combiz/scFlowData/dev-nf/assets/ctd.zip"
   reddim_genes_yml = "https://raw.githubusercontent.com/nf-core/test-datasets/scflow/refs/reddim_genes.yml"
 
   reddimplot_pointsize = 1
diff --git a/conf/test_full.config b/conf/test_full.config
old mode 100644
new mode 100755
diff --git a/docs/README.md b/docs/README.md
old mode 100644
new mode 100755
diff --git a/docs/images/nf-core-scflow_logo.png b/docs/images/nf-core-scflow_logo.png
old mode 100644
new mode 100755
diff --git a/docs/images/scflow_workflow.png b/docs/images/scflow_workflow.png
old mode 100644
new mode 100755
diff --git a/docs/output.md b/docs/output.md
old mode 100644
new mode 100755
diff --git a/docs/usage.md b/docs/usage.md
old mode 100644
new mode 100755
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
old mode 100644
new mode 100755
diff --git a/main.nf b/main.nf
old mode 100644
new mode 100755
diff --git a/modules.json b/modules.json
old mode 100644
new mode 100755
index 2462038..462d07d
--- a/modules.json
+++ b/modules.json
@@ -1,8 +1,5 @@
 {
     "name": "nf-core/scflow",
     "homePage": "https://github.com/nf-core/scflow",
-    "repos": {
-        "nf-core/modules": {
-        }
-    }
+    "repos": {}
 }
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
old mode 100644
new mode 100755
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/functions.nf b/modules/local/process/functions.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/checkinputs.nf b/modules/local/process/scflow/checkinputs.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/cluster.nf b/modules/local/process/scflow/cluster.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/dge.nf b/modules/local/process/scflow/dge.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/dirichlet.nf b/modules/local/process/scflow/dirichlet.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/finalize.nf b/modules/local/process/scflow/finalize.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/functions.nf b/modules/local/process/scflow/functions.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/integrate.nf b/modules/local/process/scflow/integrate.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/ipa.nf b/modules/local/process/scflow/ipa.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/mapcelltypes.nf b/modules/local/process/scflow/mapcelltypes.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/merge.nf b/modules/local/process/scflow/merge.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/mergeqctables.nf b/modules/local/process/scflow/mergeqctables.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/plotreddimgenes.nf b/modules/local/process/scflow/plotreddimgenes.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/qc.nf b/modules/local/process/scflow/qc.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/reducedims.nf b/modules/local/process/scflow/reducedims.nf
old mode 100644
new mode 100755
diff --git a/modules/local/process/scflow/reportintegrated.nf b/modules/local/process/scflow/reportintegrated.nf
old mode 100644
new mode 100755
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
old mode 100644
new mode 100755
diff --git a/nextflow.config b/nextflow.config
old mode 100644
new mode 100755
index c90fd42..7a7f01a
--- a/nextflow.config
+++ b/nextflow.config
@@ -18,7 +18,7 @@ manifest {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'almurphy/scfdev:0.7.1'
+process.container = 'nfancy/scflow:0.7.2'
 
 //workDir = "/rds/general/user/$USER/ephemeral/tmp"
 workDir = './work'
@@ -29,7 +29,7 @@ params {
     manifest = './refs/Manifest.txt'
     input = './refs/SampleSheet.tsv'
     ensembl_mappings = './src/ensembl-ids/ensembl_mappings.tsv'
-    ctd_path = 'https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zip'
+    ctd_path = 'https://raw.githubusercontent.com/combiz/scFlowData/dev-nf/assets/ctd.zip'
     celltype_mappings = './conf/celltype_mappings.tsv'
     reddim_genes_yml = './conf/reddim_genes.yml'
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
old mode 100644
new mode 100755
index 8771107..6ff7652
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -826,6 +826,11 @@
                     "default": 10000,
                     "description": "Max cells to sample."
                 },
+                "cta_annotation_level": {
+                    "type": "integer",
+                    "default": 1,
+                    "description": "Annotation level of the reference ctd"
+                },
                 "cta_unique_id_var": {
                     "type": "string",
                     "default": "individual",
@@ -856,6 +861,7 @@
             "required": [
                 "cta_clusters_colname",
                 "cta_cells_to_sample",
+                "cta_annotation_level",
                 "cta_unique_id_var",
                 "cta_celltype_var",
                 "cta_facet_vars",
@@ -947,13 +953,13 @@
                     "description": "Random effect confounding variable.",
                     "help_text": "If specified, the term `+ (1 | x ) +`is added to the model, where x is the specified random effects variable."
                 },
-                "dge_fc_threshold": {
+                "dge_logFC_threshold": {
                     "type": "number",
                     "default": 1.1,
                     "description": "Fold-change threshold for plotting.",
                     "help_text": "This absolute fold-change cut-off value is used in plots (e.g. volcano) and the DGE report."
                 },
-                "dge_pval_cutoff": {
+                "dge_padj_cutoff": {
                     "type": "number",
                     "default": 0.05,
                     "description": "Adjusted p-value cutoff.",
@@ -993,8 +999,8 @@
                 "dge_ref_class",
                 "dge_confounding_vars",
                 "dge_random_effects_var",
-                "dge_fc_threshold",
-                "dge_pval_cutoff",
+                "dge_logFC_threshold",
+                "dge_padj_cutoff",
                 "dge_n_label",
                 "dge_force_run",
                 "dge_max_cores"
@@ -1061,6 +1067,11 @@
                     "default": "Control,Low,High",
                     "description": "Dependent variable classes order.",
                     "help_text": "For plotting and reports, the order of classes for the dependent variable can be manually specified (e.g. 'Control,Low,High')."
+                },
+                "dirich_confounding_vars": {
+                    "type": "string",
+                    "default": "sex",
+                    "description": "Additional confounding variables."
                 }
             },
             "fa_icon": "fas fa-chart-pie",
@@ -1069,7 +1080,8 @@
                 "dirich_celltype_var",
                 "dirich_dependent_var",
                 "dirich_ref_class",
-                "dirich_var_order"
+                "dirich_var_order",
+                "dirich_confounding_vars"
             ]
         },
         "general_plotting": {
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
old mode 100644
new mode 100755
diff --git a/workflows/scflow.nf b/workflows/scflow.nf
old mode 100644
new mode 100755
index d79ff84..1901648
--- a/workflows/scflow.nf
+++ b/workflows/scflow.nf
@@ -167,6 +167,7 @@ def scflow_mapcelltypes_options      = modules['scflow_mapcelltypes']
 scflow_mapcelltypes_options.args     =
     "--clusters_colname ${params.cta_clusters_colname} \
     --cells_to_sample ${params.cta_cells_to_sample} \
+    --annotation_level ${params.cta_annotation_level} \
     --species ${params.species} \
     --reddimplot_pointsize ${params.reddimplot_pointsize} \
     --reddimplot_alpha ${params.reddimplot_alpha}"
@@ -198,8 +199,8 @@ scflow_dge_options.args              =
     --ref_class ${params.dge_ref_class} \
     --confounding_vars ${params.dge_confounding_vars} \
     --random_effects_var ${params.dge_random_effects_var} \
-    --pval_cutoff ${params.dge_pval_cutoff} \
-    --fc_threshold ${params.dge_fc_threshold} \
+    --padj_cutoff ${params.dge_padj_cutoff} \
+    --logFC_threshold ${params.dge_logFC_threshold} \
     --species ${params.species} \
     --max_cores ${params.dge_max_cores}"
 
@@ -214,8 +215,8 @@ scflow_ipa_options.args              =
     "--enrichment_tool ${params.ipa_enrichment_tool} \
     --enrichment_method ${params.ipa_enrichment_method} \
     --enrichment_database ${params.ipa_enrichment_database} \
-    --pval_cutoff ${params.dge_pval_cutoff} \
-    --fc_threshold ${params.dge_fc_threshold} \
+    --padj_cutoff ${params.dge_padj_cutoff} \
+    --logFC_threshold ${params.dge_logFC_threshold} \
     --species ${params.species}"
 
 def scflow_dirichlet_options         = modules['scflow_dirichlet']
@@ -224,7 +225,8 @@ scflow_dirichlet_options.args =
     --celltype_var ${params.dirich_celltype_var} \
     --dependent_var ${params.dirich_dependent_var} \
     --ref_class ${params.dirich_ref_class} \
-    --var_order ${params.dirich_var_order}"
+    --var_order ${params.dirich_var_order} \
+    --confounding_vars ${params.dirich_confounding_vars}"
 
 def get_software_versions         = modules['get_software_versions']
 get_software_versions.args = ''