Add script to extract umi from read name

umi.wdl

+version 1.0
+
+# Copyright (c) 2022 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task BamReadNameToUmiTag {
+
+    # This task processes a bam file with reads that have been extracted with
+    # umi-tools extract. The UMI is extracted from the read name again and put 
+    # in the bam file again with umiTag (default RX)
+    input {
+        File inputBam
+        String outputPath = "output.bam"
+        String umiTag = "RX"
+
+        String memory = "2G"
+        Int timeMinutes = 1 + ceil(size([inputBam], "G") * 10)
+        String dockerImage = "quay.io/biocontainers/pysam:0.17.0--py39h051187c_0"
+    }
+    String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
+    command <<<
+        python <<CODE
+            import pysam
+            import sys
+
+            from typing import Tuple
+
+            def split_umi_from_name(name) -> Tuple[str, str]:
+                id_and_rest = name.split(maxsplit=1)
+                if len(id_and_rest) == 1:
+                    id, = id_and_rest
+                    other_parts = ""
+                else:
+                    id, other_parts = id_and_rest
+                underscore_index = id.rfind("_")
+                umi = id[underscore_index + 1:]
+                new_id = id[:underscore_index]
+                if other_parts:
+                    return " ".join([new_id, other_parts]), umi
+                return new_id, umi
+
+            def annotate_umis(in_file, out_file, bam_tag = "RX"):
+                in_bam = pysam.AlignmentFile(in_file, "rb")
+                out_bam = pysam.AlignmentFile(out_file, "wb", template=in_bam)
+                for segment in in_bam:  # type: pysam.AlignedSegment
+                    new_name, umi = split_umi_from_name(segment.query_name)
+                    segment.query_name = new_name
+                    # append does not work. (Pysam is not Pythonic.)
+                    segment.tags = segment.tags + [(bam_tag, umi)]
+                    out_bam.write(segment)
+
+            if __name__ == "__main__":
+                annotate_umis("~{inputBam}", "~{outputPath}", "~{umiTag}")
+                pysam.index("~{outputPath}", "~{bamIndexPath}", b=True)
+        CODE
+    >>>
+
+    output {
+        File outputBam = outputBam
+        File outputBamIndex = outputBamIndex
+    }
+
+    runtime {
+        memory: memory
+        time_minutes: timeMinutes
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        # inputs
+        inputBam: {description: "The input SAM file.", category: "required"}
+        outputPath: {description: "Output directory path + output file.", category: "common"}
+        umiTag: {description: "The tag used for UMIs in the output BAM file.", category: "common"}
+
+        memory: {description: "The amount of memory available to the job.", category: "advanced"}
+        timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
+        dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
+
+        # outputs
+        outputBam: {description: "Sorted BAM file."}
+        outputBamIndex: {description: "Sorted BAM file index."}
+    }
+}