First version

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+
+## [1.0.0] - 2025-02-26
+### Added
+- [GRD-832](https://jira.oicr.on.ca/browse/GRD-871), first verion of the wdl along with README and vidarr files

Jenkinsfile

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+pipeline {
+  agent any
+  stages {
+    stage('build') {
+      when {
+        not {
+          buildingTag()
+        }
+      }
+      steps {
+        sh '/.mounts/labs/gsi/vidarr/jenkins-ci-wrapper test -t /.mounts/labs/gsi/vidarr/testing-config.json'
+      }
+    }
+    stage('Deploy') {
+      when {
+        buildingTag()
+      }
+      steps {
+        sh '/.mounts/labs/gsi/vidarr/jenkins-ci-wrapper deploy -v $TAG_NAME -t /.mounts/labs/gsi/vidarr/testing-config.json -U /.mounts/labs/gsi/vidarr/deploy-urls'
+      }
+    }
+  }
+}

README.md

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-# methyleDackel
+# methylDackel
+
+Workflow to run methylDackel, will process a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq or EM-seq alignments and extract per-base methylation metrics from them. The extract task generates bedGraph files, by default generates only CpG metrics, option can be set to also generate CHH and CHG metrics. Mbias task generates tsv file for methylation bias metrics and a svg graph for visualizing mbias (only for chromosome 1 here).
+
+## Overview
+
+## Dependencies
+
+* [methyldackel 0.6.1](https://github.com/dpryan79/MethylDackel)
+
+
+## Usage
+
+### Cromwell
+```
+java -jar cromwell.jar run methylDackel.wdl --inputs inputs.json
+```
+
+### Inputs
+
+#### Required workflow parameters:
+Parameter|Value|Description
+---|---|---
+`bam`|File|The bam file for methyl analysis
+`bai`|File|The index for input bam
+`outputFileNamePrefix`|String|Prefix for output files
+`reference`|String|The genome reference build
+
+
+#### Optional workflow parameters:
+Parameter|Value|Default|Description
+---|---|---|---
+`doMbias`|Boolean|true|Whether run Mbias or not 
+
+
+#### Optional task parameters:
+Parameter|Value|Default|Description
+---|---|---|---
+`methylDackelExtract.doCHH`|Boolean|false|whether enable CHH metrics
+`methylDackelExtract.doCHG`|Boolean|false|whether enable CHG metrics
+`methylDackelExtract.mergeContext`|Boolean|false|whether merge context in bedgraph
+`methylDackelExtract.minimumuQualityPhred`|Int?|None|minimumu sequencing quality phred score
+`methylDackelExtract.minimumMAPQ`|Int?|None|minimum MAPQ score
+`methylDackelExtract.minDepth`|Int?|None|region with minimum depth needed to be included in analysis
+`methylDackelExtract.timeout`|Int|8|The hours until the task is killed
+`methylDackelExtract.memory`|Int|8|The GB of memory provided to the task
+`methylDackelExtract.threads`|Int|8|The number of threads the task has access to
+`extractChromosomes.timeout`|Int|1|The hours until the task is killed
+`extractChromosomes.memory`|Int|1|The GB of memory provided to the task
+`extractChromosomes.threads`|Int|1|The number of threads the task has access to
+`extractChromosomes.modules`|String|"samtools/1.16.1"|The modules that will be loaded
+`methylDackelMbias.timeout`|Int|12|The hours until the task is killed
+`methylDackelMbias.memory`|Int|8|The GB of memory provided to the task
+`methylDackelMbias.threads`|Int|8|The number of threads the task has access to
+`concatMbiasTsvFiles.timeout`|Int|1|The hours until the task is killed
+`concatMbiasTsvFiles.memory`|Int|1|The GB of memory provided to the task
+`concatMbiasTsvFiles.threads`|Int|1|The number of threads the task has access to
+`concatMbiasTsvFiles.modules`|String|"pandas/2.1.3"|The modules that will be loaded
+
+
+### Outputs
+
+Output | Type | Description | Labels
+---|---|---|---
+`extract_bedgraph`|File|bedGraph output from methylDackelExtract|vidarr_label: extract_bedgraph
+`mbias_tsv`|File?|mbias tsv output from methylDackelMbias|vidarr_label: mbias_tsv
+`mbias_svg`|File?|svg plot files from methylDackelMbias|vidarr_label: mbias_svg
+
+
+## Commands
+ This section lists command(s) run by methylDackel workflow
+
+ * Running methylDackel
+
+
+ ```
+         samtools view -H ~{bam} | grep @SQ | cut -f2 | sed 's/SN://' | grep -E -v '(_random|chrUn|chrM|MT|_alt|_fix|_decoy|_PATCH|_HSCHR|NC_|_EBV|EBV|phiX|pUC19|lambda|_scaffold)'
+ ```
+ ```
+         set -euo pipefail
+         MethylDackel extract ~{filterMAPQ} ~{filterQalityPhred} ~{filterminDepth} ~{optionMergeContext} ~{optionCHH} ~{optionCHG} -@ ~{threads} ~{fasta} ~{bam} -o ~{outputFileNamePrefix}.methyldackel
+         mkdir -p ~{outputFileNamePrefix}_extract_bedGraph
+         mv *.bedGraph ~{outputFileNamePrefix}_extract_bedGraph
+         tar -czf ~{outputFileNamePrefix}_extract_bedGraph.tar.gz ~{outputFileNamePrefix}_extract_bedGraph
+ ```
+ ```
+        MethylDackel mbias --txt -r ~{chr} ~{fasta} ~{bam} ~{outputFileNamePrefix}.mbias > output_mbias.tsv
+
+        mkdir -p ~{outputFileNamePrefix}_mbias.svgs
+        mv *.svg ~{outputFileNamePrefix}_mbias.svgs
+        tar -czf ~{outputFileNamePrefix}_mbias.svgs.tar.gz ~{outputFileNamePrefix}_mbias.svgs
+ ```
+ ```
+         python3<<CODE
+
+         import sys
+         import pandas as pd
+
+         dfs = []
+         input_files = ['~{sep="', '" select_all(inputTsvs)}']
+         columns = ['Strand', 'Read', 'Position', 'nMethylated', 'nUnmethylated']
+         for file in input_files:
+             df = pd.read_csv(file, sep='\t', skiprows=1, names=columns)  # Skip header
+             dfs.append(df)
+
+         combined_df = pd.concat(dfs, ignore_index=True)
+
+         # Group by Strand, Read, and Position, and sum the methylation counts
+         aggregated_df = combined_df.groupby(['Strand', 'Read', 'Position'], as_index=False).agg({
+             'nMethylated': 'sum',
+             'nUnmethylated': 'sum'
+         }).sort_values(['Strand', 'Read', 'Position'])
+
+         with open("~{outputFileNamePrefix}.mbias.tsv", 'w') as f:
+             aggregated_df.to_csv(f, sep='\t', index=False)
+         CODE
+ ```
+ ## Support
+
+For support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to [email protected] .
+
+_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_

commands.txt

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+## Commands
+This section lists command(s) run by methylDackel workflow
+
+* Running methylDackel
+
+
+```
+        samtools view -H ~{bam} | grep @SQ | cut -f2 | sed 's/SN://' | grep -E -v '(_random|chrUn|chrM|MT|_alt|_fix|_decoy|_PATCH|_HSCHR|NC_|_EBV|EBV|phiX|pUC19|lambda|_scaffold)'
+```
+```
+        set -euo pipefail
+        MethylDackel extract ~{filterMAPQ} ~{filterQalityPhred} ~{filterminDepth} ~{optionMergeContext} ~{optionCHH} ~{optionCHG} -@ ~{threads} ~{fasta} ~{bam} -o ~{outputFileNamePrefix}.methyldackel
+        mkdir -p ~{outputFileNamePrefix}_extract_bedGraph
+        mv *.bedGraph ~{outputFileNamePrefix}_extract_bedGraph
+        tar -czf ~{outputFileNamePrefix}_extract_bedGraph.tar.gz ~{outputFileNamePrefix}_extract_bedGraph
+```
+```
+       MethylDackel mbias --txt -r ~{chr} ~{fasta} ~{bam} ~{outputFileNamePrefix}.mbias > output_mbias.tsv
+
+       mkdir -p ~{outputFileNamePrefix}_mbias.svgs
+       mv *.svg ~{outputFileNamePrefix}_mbias.svgs
+       tar -czf ~{outputFileNamePrefix}_mbias.svgs.tar.gz ~{outputFileNamePrefix}_mbias.svgs
+```
+```
+        python3<<CODE
+
+        import sys
+        import pandas as pd
+
+        dfs = []
+        input_files = ['~{sep="', '" select_all(inputTsvs)}']
+        columns = ['Strand', 'Read', 'Position', 'nMethylated', 'nUnmethylated']
+        for file in input_files:
+            df = pd.read_csv(file, sep='\t', skiprows=1, names=columns)  # Skip header
+            dfs.append(df)
+
+        combined_df = pd.concat(dfs, ignore_index=True)
+
+        # Group by Strand, Read, and Position, and sum the methylation counts
+        aggregated_df = combined_df.groupby(['Strand', 'Read', 'Position'], as_index=False).agg({
+            'nMethylated': 'sum',
+            'nUnmethylated': 'sum'
+        }).sort_values(['Strand', 'Read', 'Position'])
+
+        with open("~{outputFileNamePrefix}.mbias.tsv", 'w') as f:
+            aggregated_df.to_csv(f, sep='\t', index=False)
+        CODE
+```