add bismark/summary (#295)

* add bismark/align module

* bismark/align: add tests

* bismark/align: update meta.yml

* bismark/align: skip checksum for alignment logs

they contain timestamps

* bismark/align: restore correct checksum

caused some mixup in the last commit

* bismark/align: add genome_preparation to filters

* Fix conda version pin

* change options to be a global var

* remove params from meta.yml

* add bismark/summary

* remove md5sum check for bismark_summary_report.html

it contains a timestamp

* fix tests

* update meta.yml

* remove mysterious index files

software/bismark/summary/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bismark/summary/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BISMARK_SUMMARY {
+    label 'process_low'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? "bioconda::bismark=0.23.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bismark:0.23.0--0"
+    } else {
+        container "quay.io/biocontainers/bismark:0.23.0--0"
+    }
+
+    input:
+    path(bam)
+    path(align_report)
+    path(dedup_report)
+    path(splitting_report)
+    path(mbias)
+
+    output:
+    path("*{html,txt}")  , emit: summary
+    path  "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    """
+    bismark2summary
+
+    echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//' > ${software}.version.txt
+    """
+}

software/bismark/summary/meta.yml

@@ -0,0 +1,53 @@
+name: bismark_summary
+description: |
+    Uses Bismark report files of several samples in a run folder
+    to generate a graphical summary HTML report.
+keywords:
+    - bismark
+    - qc
+    - methylation
+    - 5mC
+    - methylseq
+    - bisulphite
+    - report
+    - summary
+tools:
+    - bismark:
+        description: |
+            Bismark is a tool to map bisulfite treated sequencing reads
+            and perform methylation calling in a quick and easy-to-use fashion.
+        homepage: https://github.com/FelixKrueger/Bismark
+        documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs
+        doi: 10.1093/bioinformatics/btr167
+input:
+    - bam:
+        type: file
+        description: Bismark alignment
+        pattern: "*.{bam}"
+    - align_report:
+        type: file
+        description: Bismark alignment reports
+        pattern: "*{report.txt}"
+    - dedup_report:
+        type: file
+        description: Bismark deduplication reports
+        pattern: "*.{deduplication_report.txt}"
+    - splitting_report:
+        type: file
+        description: Bismark splitting reports
+        pattern: "*{splitting_report.txt}"
+    - mbias:
+        type: file
+        description: Text file containing methylation bias information
+        pattern: "*.{txt}"
+output:
+    - summary:
+        type: file
+        description: Bismark summary
+        pattern: "*.{html,txt}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@phue"

tests/config/pytest_software.yml

@@ -84,6 +84,14 @@ bismark_report:
   - software/bismark/report/**
   - tests/software/bismark/report/**
 
+bismark_summary:
+  - software/bismark/genome_preparation/**
+  - software/bismark/align/**
+  - software/bismark/deduplicate/**
+  - software/bismark/methylation_extractor/**
+  - software/bismark/summary/**
+  - tests/software/bismark/summary/**
+
 blast_makeblastdb:
   - software/blast/makeblastdb/**
   - tests/software/blast/makeblastdb/**

tests/software/bismark/summary/main.nf

@@ -0,0 +1,30 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BISMARK_GENOME_PREPARATION    } from '../../../../software/bismark/genome_preparation/main.nf' addParams( options: [:] )
+include { BISMARK_ALIGN                 } from '../../../../software/bismark/align/main.nf' addParams( options: [:] )
+include { BISMARK_DEDUPLICATE           } from '../../../../software/bismark/deduplicate/main.nf' addParams( options: [:] )
+include { BISMARK_METHYLATION_EXTRACTOR } from '../../../../software/bismark/methylation_extractor/main.nf' addParams( options: [:] )
+include { BISMARK_SUMMARY               } from '../../../../software/bismark/summary/main.nf' addParams( options: [:] )
+
+workflow test_bismark_summary {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_1.fastq.gz", checkIfExists: true),
+                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_methylated_2.fastq.gz", checkIfExists: true) ] ]
+
+    BISMARK_GENOME_PREPARATION ( file("${launchDir}/tests/data/genomics/sarscov2/fasta/test_genome.fasta", checkIfExists: true) )
+    BISMARK_ALIGN ( input, BISMARK_GENOME_PREPARATION.out.index )
+    BISMARK_DEDUPLICATE ( BISMARK_ALIGN.out.bam )
+    BISMARK_METHYLATION_EXTRACTOR ( BISMARK_DEDUPLICATE.out.bam, BISMARK_GENOME_PREPARATION.out.index )
+
+    BISMARK_SUMMARY (
+        BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam },
+        BISMARK_ALIGN.out.report.collect{ meta, report -> report },
+        BISMARK_DEDUPLICATE.out.report.collect{ meta, bam -> bam },
+        BISMARK_METHYLATION_EXTRACTOR.out.report.collect{ meta, report -> report },
+        BISMARK_METHYLATION_EXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
+    )
+}

tests/software/bismark/summary/test.yml

@@ -0,0 +1,9 @@
+- name: Run bismark summary test workflow
+  command: nextflow run ./tests/software/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
+  tags:
+    - bismark
+    - bismark_summary
+  files:
+    - path: output/bismark/bismark_summary_report.html
+    - path: output/bismark/bismark_summary_report.txt
+      md5sum: 06fc717e81b3f8f0d6e279d572f407f6