From 3acdf937c06a5f78c33977348909606672f60cc3 Mon Sep 17 00:00:00 2001
From: Juan Puerto <=>
Date: Wed, 10 Apr 2024 10:59:02 -0400
Subject: [PATCH] General: Add WDL translations for pipeline and salmon-quant
 for testing

---
 pipeline.wdl                    |  31 ++++++
 steps/salmon-quantification.wdl | 170 ++++++++++++++++++++++++++++++++
 2 files changed, 201 insertions(+)
 create mode 100644 pipeline.wdl
 create mode 100644 steps/salmon-quantification.wdl

diff --git a/pipeline.wdl b/pipeline.wdl
new file mode 100644
index 0000000..cd0d9f0
--- /dev/null
+++ b/pipeline.wdl
@@ -0,0 +1,31 @@
+## Use double '#' for workflow-level comments
+## This workflow implements a one-task workflow
+
+# write the WDL version number 'version 1.0' -- 1
+# possible to write 'WDL developent' as a version number as well
+version development
+
+# create a workflow named 'HelloWorld' -- 2
+import "./steps/salmon-quantification.wdl" as SalmonQuantification
+workflow SalmonRNAseq {
+    input {
+        Array[Directory] fastq_dir
+        Directory? img_dir
+        Directory? metadata_dir
+        String assay
+        Int threads
+        Int? expected_cell_count
+        Boolean? keep_all_barcodes
+    }
+
+    call SalmonQuantification.SalmonQuantification {
+        input:
+            fastq_dir = fastq_dir,
+            img_dir = img_dir,
+            metadata_dir = metadata_dir,
+            assay = assay,
+            threads = threads,
+            expected_cell_count = expected_cell_count,
+            keep_all_barcodes = keep_all_barcodes
+    }
+}
diff --git a/steps/salmon-quantification.wdl b/steps/salmon-quantification.wdl
new file mode 100644
index 0000000..d12d340
--- /dev/null
+++ b/steps/salmon-quantification.wdl
@@ -0,0 +1,170 @@
+version development
+
+workflow SalmonQuantification {
+    input {
+        Array[Directory] fastq_dir
+        Directory? img_dir
+        Directory? metadata_dir
+        String assay
+        Int threads
+        Int? expected_cell_count
+        Boolean? keep_all_barcodes
+    }
+
+    output {
+        Directory salmon_output = Salmon.output_dir
+        File count_matrix_h5ad = AnnotateCells.annotated_h5ad_file
+        File? raw_count_matrix = AlevinToAnndata.raw_expr_h5ad
+        File genome_build_json = AlevinToAnndata.genome_build_json
+    }
+
+    call AdjustBarcodes{
+      input:
+        assay = assay,
+        fastq_dir = fastq_dir
+    }
+
+    call TrimReads {
+        input:
+            assay = assay,
+            adj_fastq_dir = AdjustBarcodes.adj_fastq_dir,
+            orig_fastq_dirs = fastq_dir,
+            threads = threads
+    }
+
+    call Salmon {
+        input:
+            orig_fastq_dirs = fastq_dir,
+            trimmed_fastq_dir = TrimReads.trimmed_fastq_dir,
+            assay = assay,
+            threads = threads,
+            expected_cell_count = expected_cell_count,
+            keep_all_barcodes = keep_all_barcodes
+    }
+
+    call AlevinToAnndata {
+        input:
+            assay = assay,
+            alevin_dir = Salmon.output_dir
+    }
+
+    call AnnotateCells {
+        input:
+            assay = assay,
+            orig_fastq_dirs = fastq_dir,
+            h5ad_file = AlevinToAnndata.expr_h5ad,
+            img_dir = img_dir,
+            metadata_dir = metadata_dir,
+            metadata_json = AdjustBarcodes.metadata_json
+    }
+}
+
+task AdjustBarcodes {
+    input {
+        String assay
+        Array[Directory] fastq_dir
+    }
+
+    output {
+        Directory adj_fastq_dir = "adj_fastq"
+        File? metadata_json = "metadata.json"
+    }
+
+    command {
+        /opt/adjust_barcodes.py ~{assay} directory ~{sep(" ", fastq_dir)}
+    }
+
+    runtime {
+        container: "hubmap/scrna-barcode-adj:latest"
+    }
+}
+
+task TrimReads {
+    input {
+        String assay
+        Directory adj_fastq_dir
+        Array[Directory] orig_fastq_dirs
+        Int threads
+    }
+
+    output {
+        Directory trimmed_fastq_dir = "trimmed"
+    }
+
+    runtime {
+        container: "hubmap/scrna-trim-reads:latest"
+    }
+
+    command {
+        /opt/trim_reads.py ~{assay} ~{adj_fastq_dir} ~{sep(" ", orig_fastq_dirs)}
+    }
+}
+
+task Salmon {
+    input {
+        String assay
+        Directory trimmed_fastq_dir
+        Array[Directory] orig_fastq_dirs
+        Int threads
+        Int? expected_cell_count
+        Boolean? keep_all_barcodes
+    }
+
+    output {
+        Directory output_dir = "salmon_out"
+    }
+
+    runtime {
+        container: "hubmap/salmon-grch38:latest"
+    }
+
+    command {
+        /opt/salmon_wrapper.py ~{assay} ~{trimmed_fastq_dir} ~{sep(" ", orig_fastq_dirs)} --threads ~{threads} ~{if defined(expected_cell_count) then "--expected-cell-count " + expected_cell_count else ""} ~{if defined(keep_all_barcodes) then "--keep-all-barcodes " + keep_all_barcodes else ""}
+    }
+}
+
+task AlevinToAnndata {
+    input {
+        String assay
+        Directory alevin_dir
+    }
+
+    output {
+        File? raw_expr_h5ad = "raw_expr.h5ad"
+        File expr_h5ad = "expr.h5ad"
+        File genome_build_json = "genome_build.json"
+    }
+
+    runtime {
+        container: "hubmap/scrna-analysis:latest"
+    }
+
+    # Need to fix this command
+    command {
+        /opt/alevin_to_anndata.py ~{assay} ~{alevin_dir}
+    }
+}
+
+task AnnotateCells {
+    input {
+        String assay
+        File h5ad_file
+        Array[Directory] orig_fastq_dirs
+        Directory? img_dir
+        Directory? metadata_dir
+        File? metadata_json
+    }
+
+    output {
+        File annotated_h5ad_file = "expr.h5ad"
+    }
+
+    runtime {
+        container: "hubmap/scrna-analysis:latest"
+    }
+
+    # Need to fix this command
+    command {
+        /opt/annotate_cells.py
+    }
+}
\ No newline at end of file