adding new pipe

mop_dna/comparison.tsv

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+CO_22_K1	CO_22_S1

mop_dna/config.yaml

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+title: "Master of Pores"
+subtitle: ""
+intro_text: False
+
+report_header_info:
+    - Application Type: 'Nanopore sequencing'
+
+custom_logo: 'logo_small.png'
+custom_logo_url: 'https://github.com/biocorecrg/nanopore_analysis'
+custom_logo_title: 'Master of Pores'
+
+extra_fn_clean_trim:
+   - '_QC'
+
+table_columns_visible:
+    FastQC:
+        percent_duplicates: True
+
+module_order:
+ - fastqc:
+        name: 'FastQC'
+        info: 'This section of the report shows FastQC results on raw reads.'
+
+ - alnQC:
+        name: "alnQC"
+        info: 'This section of the report shows alnQC results on aligned reads'

mop_dna/mop_dna.nf

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+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+/*
+ * Define the pipeline parameters
+ *
+ */
+
+// Pipeline version
+version = '3.0'
+
+params.help            = false
+params.resume          = false
+
+log.info """
+
+╔╦╗┌─┐╔═╗  ╔╦╗╔╗╔╔═╗
+║║║│ │╠═╝   ║║║║║╠═╣
+╩ ╩└─┘╩    ═╩╝╝╚╝╩ ╩
+
+====================================================
+BIOCORE@CRG Master of Pores 3. Detection of DNA variations - N F  ~  version ${version}
+====================================================
+
+*****************   Input files    *******************
+input_path                              : ${params.input_path}
+comparison                              : ${params.comparison}
+
+********** reference has to be the genome *************
+reference                               : ${params.reference}
+output                                  : ${params.output}
+pars_tools                              : ${params.pars_tools}
+
+************************* Flows *******************************
+clairS                                  : ${params.clairS}
+
+email                                   : ${params.email}
+"""
+
+// Help and avoiding typos
+if (params.help) exit 1
+if (params.resume) exit 1, "Are you making the classical --resume typo? Be careful!!!! ;)"
+
+// check input files
+reference = file(params.reference)
+if( !reference.exists() ) exit 1, "Missing reference file: ${reference}!"
+
+// include functions, outdirs from other files
+evaluate(new File("../outdirs.nf"))
+def local_modules = file("$baseDir/../local_modules.nf")
+
+def subworkflowsDir = "${baseDir}/../BioNextflow/subworkflows"
+
+def flows = [:]
+flows["clairS"] = params.clairS
+
+include { getParameters; mapIDPairs } from "${local_modules}"
+include { final_message; notify_slack } from "${subworkflowsDir}/global_functions.nf"
+include { checkRef } from "${local_modules}"
+
+// Create a channel for tool options
+progPars = getParameters(params.pars_tools)
+
+include { RUN as RUN_CLAIRS } from "${subworkflowsDir}/snp_calling/clairS" addParams(LABEL: 'big_mem_cpus', EXTRAPARS: progPars["clairS--clairS"], OUTPUT: outputClairS)
+
+
+
+/*
+ * Creates the channels with comparisons
+ */
+
+comparisons = channel.empty()
+
+if (params.comparison != "") {
+   compfile = file(params.comparison)
+   if( !compfile.exists() ) exit 1, "Missing comparison file: ${compfile}. Specify path with --comparisons"
+
+   Channel
+    .from(compfile.readLines())
+    .map { line ->
+        list = line.split("\t")
+        if (list.length <2) {
+            error "ERROR!!! Comparison file has to be tab separated\n"
+        }
+        if (list[0]!= "") {
+            def sampleID = list[0]
+            def ctrlID = list[1]
+            [ sampleID, ctrlID ]
+        }
+    }.set {comparisons}
+}
+
+
+workflow {
+    // Get Sample Names from comparisons
+    comparisons.flatten().unique().set{unique_samples}
+    // get BAM FILEs
+    unique_samples.map {
+         [it, file("${params.input_path}/alignment/${it}_s.bam")]
+    }.transpose().set{bams}
+    // get BAI FILEs
+    unique_samples.map {
+         [it, file("${params.input_path}/alignment/${it}_s.bam.bai")]
+    }.transpose().set{bais}
+
+   // ref_file = checkRef(reference)
+   clairS_flow(bams, comparisons, reference)
+
+
+}
+
+
+workflow clairS_flow {
+
+    take:
+    bam
+    comparisons
+    reference
+
+    main:
+    data = mapIDPairs(comparisons, bam)
+    RUN_CLAIRS(data, reference)
+
+//    emit:
+
+}
+
+
+
+
+workflow.onComplete {
+
+    def text = final_message("MoP3")
+    println text
+    if (params.hook != "") {
+       notify_slack(text, params.hook)
+    }
+}
+
+/*
+* Mail notification
+*/
+
+if (params.email == "yourmail@yourdomain" || params.email == "") {
+    log.info 'Skipping the email\n'
+}
+else {
+    log.info "Sending the email to ${params.email}\n"
+
+    workflow.onComplete {
+
+    def msg = """\
+        Pipeline BIOCORE@CRG Master of Pore 3 modification module's execution summary
+        ---------------------------
+        Completed at: ${workflow.complete}
+        Duration    : ${workflow.duration}
+        Success     : ${workflow.success}
+        workDir     : ${workflow.workDir}
+        exit status : ${workflow.exitStatus}
+        Error report: ${workflow.errorReport ?: '-'}
+        """
+        .stripIndent()
+
+        sendMail(to: params.email, subject: "Master of Pore 3 execution", body: msg)
+    }
+}

mop_dna/nextflow.config

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+includeConfig "../nextflow.global.config"
+//singularity.cacheDir = "$baseDir/../singularity"

mop_dna/params.yaml

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+input_path: "${projectDir}/test_dataset/"
+comparison: "${projectDir}/comparison.tsv"
+
+reference: "/db/gencode/human/release_38/GRCh38.primary_assembly.genome.fa.gz"
+output: "${projectDir}/output_dna"
+pars_tools: "${projectDir}/tools_opt.tsv"
+
+# flows
+clairS: "YES"
+
+# epinano plots
+hook: ""
+email: ""

mop_dna/tools_opt.tsv

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+#flows	tool	extrapars
+clairS	clairS	"-p ont_r9_guppy"