Merge pull request #139 from biowdl/BIOWDL-258

BIOWDL-258: Add WDL task for Minimap2

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ Add WDL task for Minimap2
 + Add WDL task for TALON
 + Add WDL task for TranscriptClean
 + Fastqsplitter: fix mkdir command to work with biocontainer's busybox mkdir

minimap2.wdl

+version 1.0
+
+# Copyright (c) 2019 Sequencing Analysis Support Core - 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 Indexing {
+    input {
+        File referenceFile
+        String outputPrefix
+        Boolean useHomopolymerCompressedKmer = false
+        Int kmerSize = 15
+        Int minimizerWindowSize = 10
+
+        Int? splitIndex
+
+        Int cores = 1
+        Int memory = 4
+        String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputPrefix})
+        minimap2 \
+        ~{true="-H" false="" useHomopolymerCompressedKmer} \
+        ~{"-k " + kmerSize} \
+        ~{"-w " + minimizerWindowSize} \
+        ~{"-I " + splitIndex} \
+        ~{"-d " + outputPrefix + ".mmi"} \
+        ~{"-t " + cores} \
+        ~{referenceFile}
+    }
+
+    output {
+        File outputIndexFile = outputPrefix + ".mmi"
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        referenceFile: "Reference fasta file."
+        outputPrefix: "Output directory path + output file prefix."
+        useHomopolymerCompressedKmer: "Use homopolymer-compressed k-mer (preferrable for PacBio)."
+        kmerSize: "K-mer size (no larger than 28)."
+        minimizerWindowSize: "Minimizer window size."
+        splitIndex: "Split index for every ~NUM input bases."
+
+        outputIndexFile: "Indexed reference file."
+    }
+}
+
+task Mapping {
+    input {
+        File queryFile
+        File referenceFile
+        String outputPrefix
+        String presetOption
+        Boolean outputSAM = false
+
+        Int? maxFragmentLength
+        Int? maxIntronLength
+        Boolean? skipSelfAndDualMappings
+        Int? retainMaxSecondaryAlignments
+        Int? matchingScore
+        Int? mismatchPenalty
+        String? howToFindGTAG
+        Boolean? secondaryAlignment
+
+        Int cores = 4
+        Int memory = 7
+        String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
+    }
+
+    command {
+        set -e
+        mkdir -p $(dirname ~{outputPrefix})
+        minimap2 \
+        ~{"-x " + presetOption} \
+        ~{true="-a" false="" outputSAM} \
+        ~{"-G " + maxIntronLength} \
+        ~{"-F " + maxFragmentLength} \
+        ~{true="-X" false="" skipSelfAndDualMappings} \
+        ~{"-N " + retainMaxSecondaryAlignments} \
+        ~{"-A " + matchingScore} \
+        ~{"-B " + mismatchPenalty} \
+        ~{"-u " + howToFindGTAG} \
+        --secondary=~{true="yes" false="no" secondaryAlignment} \
+        ~{"-o " + outputPrefix} \
+        ~{"-t " + cores} \
+        ~{referenceFile} \
+        ~{queryFile}
+    }
+
+    output {
+        File outputAlignmentFile = outputPrefix
+    }
+
+    runtime {
+        cpu: cores
+        memory: memory
+        docker: dockerImage
+    }
+
+    parameter_meta {
+        queryFile: "Input fasta file."
+        referenceFile: "Reference fasta file."
+        outputPrefix: "Output directory path + output file prefix."
+        presetOption: "This option applies multiple options at the same time."
+        outputSAM: "Output in the SAM format."
+        maxFragmentLength: "Max fragment length (effective with -xsr or in the fragment mode)."
+        maxIntronLength: "Max intron length (effective with -xsplice; changing -r)."
+        skipSelfAndDualMappings: "Skip self and dual mappings (for the all-vs-all mode)."
+        retainMaxSecondaryAlignments: "Retain at most INT secondary alignments."
+        matchingScore: "Matching score."
+        mismatchPenalty: "Mismatch penalty."
+        howToFindGTAG: "How to find GT-AG. f:transcript strand, b:both strands, n:don't match GT-AG."
+        secondaryAlignment: "Whether to output secondary alignments."
+
+        outputAlignmentFile: "Mapping and alignment between collections of DNA sequences file."
+    }
+}