updated with scflow v0.7.2

combiz · Apr 13, 2023 · 6461311 · 6461311
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Showing 70 changed files with 39 additions and 22 deletions.
diff --git a/.editorconfig b/.editorconfig
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
diff --git a/.gitignore b/.gitignore
diff --git a/.markdownlint.yml b/.markdownlint.yml
diff --git a/.nf-core.yml b/.nf-core.yml
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CITATIONS.md b/CITATIONS.md
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/assets/NO_FILE.tsv b/assets/NO_FILE.tsv
diff --git a/assets/email_template.html b/assets/email_template.html
diff --git a/assets/email_template.txt b/assets/email_template.txt
diff --git a/assets/nf-core-scflow_logo.png b/assets/nf-core-scflow_logo.png
diff --git a/assets/schema_input.json b/assets/schema_input.json
diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt
diff --git a/bin/scflow_dge.r b/bin/scflow_dge.r
@@ -131,15 +131,15 @@ required$add_argument(
 )
 
 required$add_argument(
-  "--fc_threshold",
+  "--logFC_threshold",
   type = "double",
   default = 1.1,
   metavar = "number",
   help = "Absolute fold-change cutoff for DE [default %(default)s]"
 )
 
 required$add_argument(
-  "--pval_cutoff",
+  "--padj_cutoff",
   type = "double",
   default = 0.05,
   metavar = "number",
@@ -254,8 +254,6 @@ de_results <- perform_de(
   ref_class = args$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_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,
   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$padj_cutoff,
+      abs(logFC) >= log2(args$logFC_threshold)
     )
 
   if (nrow(dt) < 5) {

diff --git 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
@@ -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
diff --git a/conf/gcp.config b/conf/gcp.config
diff --git a/conf/igenomes.config b/conf/igenomes.config
diff --git a/conf/modules.config b/conf/modules.config
diff --git a/conf/scflow_analysis.config b/conf/scflow_analysis.config
@@ -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'

diff --git a/conf/test.config b/conf/test.config
diff --git a/conf/test_full.config b/conf/test_full.config
diff --git a/docs/README.md b/docs/README.md
diff --git a/docs/images/nf-core-scflow_logo.png b/docs/images/nf-core-scflow_logo.png
diff --git a/docs/images/scflow_workflow.png b/docs/images/scflow_workflow.png
diff --git a/docs/output.md b/docs/output.md
diff --git a/docs/usage.md b/docs/usage.md
diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar
diff --git a/main.nf b/main.nf
diff --git a/modules.json b/modules.json
diff --git a/modules/local/functions.nf b/modules/local/functions.nf
diff --git a/modules/local/get_software_versions.nf b/modules/local/get_software_versions.nf
diff --git a/modules/local/process/functions.nf b/modules/local/process/functions.nf
diff --git a/modules/local/process/scflow/checkinputs.nf b/modules/local/process/scflow/checkinputs.nf
diff --git a/modules/local/process/scflow/cluster.nf b/modules/local/process/scflow/cluster.nf
diff --git a/modules/local/process/scflow/dge.nf b/modules/local/process/scflow/dge.nf
diff --git a/modules/local/process/scflow/dirichlet.nf b/modules/local/process/scflow/dirichlet.nf
diff --git a/modules/local/process/scflow/finalize.nf b/modules/local/process/scflow/finalize.nf
diff --git a/modules/local/process/scflow/functions.nf b/modules/local/process/scflow/functions.nf
diff --git a/modules/local/process/scflow/integrate.nf b/modules/local/process/scflow/integrate.nf
diff --git a/modules/local/process/scflow/ipa.nf b/modules/local/process/scflow/ipa.nf
diff --git a/modules/local/process/scflow/mapcelltypes.nf b/modules/local/process/scflow/mapcelltypes.nf
diff --git a/modules/local/process/scflow/merge.nf b/modules/local/process/scflow/merge.nf
diff --git a/modules/local/process/scflow/mergeqctables.nf b/modules/local/process/scflow/mergeqctables.nf
diff --git a/modules/local/process/scflow/plotreddimgenes.nf b/modules/local/process/scflow/plotreddimgenes.nf
diff --git a/modules/local/process/scflow/qc.nf b/modules/local/process/scflow/qc.nf
diff --git a/modules/local/process/scflow/reducedims.nf b/modules/local/process/scflow/reducedims.nf
diff --git a/modules/local/process/scflow/reportintegrated.nf b/modules/local/process/scflow/reportintegrated.nf
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
diff --git a/nextflow.config b/nextflow.config
diff --git 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"

diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
diff --git 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']