Adding files for Peddy analysis

.dockstore.yml

@@ -119,6 +119,31 @@ workflows:
    primaryDescriptorPath: /CleanupFailedSubmissions/Cleanup_Failed_Submissions.wdl
    testParameterFiles:
     - /CleanupFailedSubmissions/Cleanup_Failed_Submissions.inputs.json
+ - name: codec_bcl2fastq
+   subclass: WDL
+   primaryDescriptorPath: /CODEC/codec_bcl2fastq.wdl
+   testParameterFiles:
+    - /CODEC/codec_bcl2fastq.inputs.json
+ - name: demux_CODEC
+   subclass: WDL
+   primaryDescriptorPath: /CODEC/demux_CODEC.wdl
+   testParameterFiles:
+    - /CODEC/demux_CODEC.inputs.json
+ - name: SingleSampleCODEC
+   subclass: WDL
+   primaryDescriptorPath: /CODEC/SingleSampleCODEC.wdl
+   testParameterFiles:
+    - /CODEC/SingleSampleCODEC.inputs.json
+ - name: SigProfiler
+   subclass: WDL
+   primaryDescriptorPath: /CODEC/SigProfiler.wdl
+   testParameterFiles:
+    - /CODEC/SigProfiler.inputs.json
+ - name: Peddy_AnalysisFamiliarRelatedness
+   subclass: WDL
+   primaryDescriptorPath: /PeddyAnalysis/Peddy_AnalyzeFamilialRelateness.wdl
+   testParameterFiles:
+    - /PeddyAnalysis/Peddy_AnalyzeFamilialRelateness.inputs.json
  - name: TAG_Mop
    subclass: WDL
    primaryDescriptorPath: /TAG_Mop/TAG_Mop.wdl

CODEC/README.md

@@ -0,0 +1,19 @@
+# Signature Profiling WDL for CODEC Mutlist Output
+CODEC pipeline: SingleSampleCODEC pipeline provides text files for discovered mutations. 
+
+This workflow summarizes and plots mutation spectrums in 96 trinucleotide contexts and generate Mutation Matrix that will be later used to subtract SBS(Single Base Substitution) signatures from SNVs with database reference from COSMIC(https://cancer.sanger.ac.uk/signatures/).
+
+The Signature Profiling tool is from https://github.com/AlexandrovLab/SigProfilerAssignment and has been implanted to the docker image.
+
+The output of this WDL includes: 
+1) SpectrumPlots
+2) MutationMetrics
+3) SignatureCount
+4) SignatureProportionPDF
+5) SignatureStackedPlot
+6) TMBPlot
+7) DecomposedSignatureProbabilities
+
+
+### Citation
+Díaz-Gay et al. 2023 Bioinformatics and Tate et al. 2019 Nucleic Acids Research

CODEC/SigProfiler.inputs.json

@@ -0,0 +1 @@
+{"SigProfiler.GenomeFasta":"${workspace.referenceData_hg38_ref_fasta}","SigProfiler.MutlistFiles":"${this.samples.variants_called}","SigProfiler.mutlist_to_96_contexts.GenomeFastaIndex":"${workspace.referenceData_hg38_ref_fasta_index}"}

CODEC/SigProfiler.wdl

@@ -0,0 +1,145 @@
+version 1.0
+
+workflow SigProfiler {
+    input {
+        Array[File] MutlistFiles
+        File GenomeFasta
+    }
+
+    call mutlist_to_96_contexts {
+        input:
+            MutlistFiles = MutlistFiles,
+            GenomeFasta = GenomeFasta
+    }
+    call sigprofiler_analysis {
+        input: 
+            MutationMetrics = mutlist_to_96_contexts.MutationMetrics
+
+    }
+    call PlotSignatures {
+        input: 
+            SignatureCount = sigprofiler_analysis.SignatureCount
+    }
+
+    output {
+        File MutationMetrics = mutlist_to_96_contexts.MutationMetrics
+        File SpectrumPlots = mutlist_to_96_contexts.SpectrumPlots
+        File DecomposedSignatureProbabilities = sigprofiler_analysis.DecomposedSignatureProbabilities
+        File SignatureStackedPlot = sigprofiler_analysis.SignatureStackedPlot
+        File TMBPlot = sigprofiler_analysis.TMBPlot
+        File SignatureCount = sigprofiler_analysis.SignatureCount
+        File SignatureProportionPDF = PlotSignatures.signature_proportions_pdf
+    }
+}
+
+
+
+task mutlist_to_96_contexts {
+    input {
+        Array[File] MutlistFiles
+        File GenomeFasta
+        File GenomeFastaIndex
+    }
+
+    command {
+        Rscript /scripts/96_contexts_mutations.R "~{sep=' ' MutlistFiles}" ~{GenomeFasta}
+    }
+
+    output {
+        File MutationMetrics = "trinuc_mutation_metrics.txt"
+        File SpectrumPlots = "all_sample_spectrums.pdf"
+    }
+
+    runtime {
+        docker: "us.gcr.io/tag-public/sigprofiler:v1"
+        memory: "8 GB"
+        disks: "local-disk 20 HDD"
+    }
+}
+
+task sigprofiler_analysis {
+    input {
+        File MutationMetrics
+        String OutputFolder = "SigProfiler-output"
+    }
+
+    command {
+        python3 <<EOF
+        import sys
+        from SigProfilerMatrixGenerator import install as genInstall
+        genInstall.install("GRCh38")
+
+        from SigProfilerAssignment import Analyzer as Analyze
+        Analyze.cosmic_fit(samples="~{MutationMetrics}",
+                           output="~{OutputFolder}",
+                           input_type="matrix",
+                           genome_build="GRCh38",
+                           cosmic_version=3.3)
+        EOF
+    }
+
+    output {
+        File DecomposedSignatureProbabilities = "~{OutputFolder}/Assignment_Solution/Activities/Decomposed_MutationType_Probabilities.txt"
+        File SignatureStackedPlot = "~{OutputFolder}/Assignment_Solution/Activities/Assignment_Solution_Activity_Plots.pdf"
+        File TMBPlot = "~{OutputFolder}/Assignment_Solution/Activities/Assignment_Solution_TMB_plot.pdf"
+        File SignatureCount = "~{OutputFolder}/Assignment_Solution/Activities/Assignment_Solution_Activities.txt"
+    }
+
+    runtime {
+        docker: "us.gcr.io/tag-public/sigprofiler:v1"
+        memory: "8 GB"
+        disks: "local-disk 20 HDD"
+    }
+}
+
+
+task PlotSignatures {
+  input {
+    File SignatureCount
+  }
+
+  command {
+    python3 <<EOF
+    import pandas as pd
+    import matplotlib.pyplot as plt
+    import seaborn as sns
+
+    SigCounts = pd.read_csv("${SignatureCount}", sep='\t', header=0)
+    SigCounts = pd.DataFrame(SigCounts)
+
+    # Calculate proportions
+    signature_cols = SigCounts.columns[1:]  # Exclude the 'Samples' column
+    SigCounts[signature_cols] = SigCounts[signature_cols].div(SigCounts[signature_cols].sum(axis=1), axis=0)
+
+    # Reshape the data
+    SigCounts_long = SigCounts.melt(id_vars=["Samples"], var_name="Signature", value_name="Proportion")
+    SigCounts_long = SigCounts_long[SigCounts_long["Proportion"] > 0]
+
+    # Plot the data
+    plt.figure(figsize=(16, 9))
+    sns.scatterplot(data=SigCounts_long, x="Samples", y="Signature", size="Proportion", sizes=(20, 200), legend=False)
+    plt.xticks(rotation=90)
+    plt.xlabel("Sample Name", fontsize=16)
+    plt.ylabel("Signature", fontsize=16)
+    plt.title("Signature Proportions by Sample", fontsize=20, pad = 20)
+    plt.grid(axis='y')
+    ax = plt.gca()
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+    ax.spines['left'].set_visible(False)
+    ax.spines['bottom'].set_visible(False)
+    plt.tight_layout()
+    plt.savefig("signature_proportions.pdf", format="pdf")
+    EOF
+  }
+
+  output {
+    File signature_proportions_pdf = "signature_proportions.pdf"
+  }
+
+  runtime {
+        docker: "us.gcr.io/tag-public/sigprofiler:v1"
+        memory: "8 GB"
+        disks: "local-disk 20 HDD"
+  }
+}

CODEC/SingleSampleCODEC.inputs.json

@@ -0,0 +1,63 @@
+{
+    "SingleSampleCODEC.AlignMolecularConsensusReads.cpu_cores": "${2}",
+    "SingleSampleCODEC.AlignMolecularConsensusReads.disk_size": "${}",
+    "SingleSampleCODEC.AlignMolecularConsensusReads.memory": "${}",
+    "SingleSampleCODEC.AlignMolecularConsensusReads.threads": "${8}",
+    "SingleSampleCODEC.AlignRawTrimmed.disk": "${64}",
+    "SingleSampleCODEC.AlignRawTrimmed.disk_size": "${}",
+    "SingleSampleCODEC.AlignRawTrimmed.mem": "${}",
+    "SingleSampleCODEC.AlignRawTrimmed.memory": "${64}",
+    "SingleSampleCODEC.CDSByProduct.disk_size": "${}",
+    "SingleSampleCODEC.CDSByProduct.mem": "${}",
+    "SingleSampleCODEC.CSS_SFC_ErrorMetrics.disk_size": "${800}",
+    "SingleSampleCODEC.CSS_SFC_ErrorMetrics.memory": "${}",
+    "SingleSampleCODEC.CollectConsensusWgsMetrics.disk_size": "${160}",
+    "SingleSampleCODEC.CollectConsensusWgsMetrics.memory": "${}",
+    "SingleSampleCODEC.CollectInsertSizeMetrics.disk_size": "${100}",
+    "SingleSampleCODEC.CollectInsertSizeMetrics.memory": "${32}",
+    "SingleSampleCODEC.CollectRawWgsMetrics.disk_size": "${160}",
+    "SingleSampleCODEC.CollectRawWgsMetrics.memory": "${}",
+    "SingleSampleCODEC.FgbioCollapseReadFamilies.disk_size": "${200}",
+    "SingleSampleCODEC.FgbioCollapseReadFamilies.memory": "${}",
+    "SingleSampleCODEC.GroupReadByUMI.disk_size": "${400}",
+    "SingleSampleCODEC.GroupReadByUMI.memory": "${32}",
+    "SingleSampleCODEC.MarkRawDuplicates.disk_size": "${200}",
+    "SingleSampleCODEC.MarkRawDuplicates.memory": "${64}",
+    "SingleSampleCODEC.MergeAndSortMoleculeConsensusReads.disk_size": "${160}",
+    "SingleSampleCODEC.MergeAndSortMoleculeConsensusReads.memory": "${64}",
+    "SingleSampleCODEC.MergeLogSplit.disk_size": "${}",
+    "SingleSampleCODEC.MergeLogSplit.mem": "${}",
+    "SingleSampleCODEC.MergeSplit.disk_size": "${200}",
+    "SingleSampleCODEC.MergeSplit.memory": "${32}",
+    "SingleSampleCODEC.RAW_SFC_ErrorMetrics.disk_size": "${800}",
+    "SingleSampleCODEC.RAW_SFC_ErrorMetrics.memory": "${32}",
+    "SingleSampleCODEC.ReplaceRawReadGroup.disk_size": "${200}",
+    "SingleSampleCODEC.ReplaceRawReadGroup.memory": "${32}",
+    "SingleSampleCODEC.SortBam.disk_size": "${200}",
+    "SingleSampleCODEC.SortBam.mem": "${}",
+    "SingleSampleCODEC.SplitFastq1.disk_size": "${400}",
+    "SingleSampleCODEC.SplitFastq1.memory": "${32}",
+    "SingleSampleCODEC.SplitFastq2.disk_size": "${400}",
+    "SingleSampleCODEC.SplitFastq2.memory": "${32}",
+    "SingleSampleCODEC.Trim.disk_size": "${64}",
+    "SingleSampleCODEC.Trim.mem": "${32}",
+    "SingleSampleCODEC.ZipperBamAlignment.disk_size": "${200}",
+    "SingleSampleCODEC.ZipperBamAlignment.mem": "${32}",
+    "SingleSampleCODEC.eval_genome_bed": "gs://gptag/CODEC/ddbtp_codec_easy_regions.hg38.bed",
+    "SingleSampleCODEC.eval_genome_interval": "gs://gptag/CODEC/ddbtp_codec_easy_regions.hg38.interval_list",
+    "SingleSampleCODEC.fastq1": "${this.fastq1}",
+    "SingleSampleCODEC.fastq2": "${this.fastq2}",
+    "SingleSampleCODEC.germline_bam": "${this.germline_bam}",
+    "SingleSampleCODEC.germline_bam_index": "${this.germline_bam_index}",
+    "SingleSampleCODEC.num_parallel": "${40}",
+    "SingleSampleCODEC.reference_amb": "${workspace.referenceData_hg38_ref_amb}",
+    "SingleSampleCODEC.reference_ann": "${workspace.referenceData_hg38_ref_ann}",
+    "SingleSampleCODEC.reference_bwt": "${workspace.referenceData_hg38_ref_bwt}",
+    "SingleSampleCODEC.reference_dict": "${workspace.referenceData_hg38_ref_dict}",
+    "SingleSampleCODEC.reference_fasta": "${workspace.referenceData_hg38_ref_fasta}",
+    "SingleSampleCODEC.reference_fasta_index": "${workspace.referenceData_hg38_ref_fasta_index}",
+    "SingleSampleCODEC.reference_pac": "${workspace.referenceData_hg38_ref_pac}",
+    "SingleSampleCODEC.reference_sa": "${workspace.referenceData_hg38_ref_sa}",
+    "SingleSampleCODEC.sample_id": "${this.sample_id}",
+    "SingleSampleCODEC.sort_memory": "2G"
+}