Add plasmidid module (#410)

* Adding plasmidid module

* Adding test for plasmidid module

* Update plasmidid version to 1.6.4

* Adding contigs.fasta file

* Update tests

* Adding output files on test.yml

software/plasmidid/functions.nf

@@ -0,0 +1,60 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.args3         = args.args3 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/plasmidid/main.nf

@@ -0,0 +1,50 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process PLASMIDID {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? 'bioconda::plasmidid=1.6.4' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/plasmidid:1.6.4--hdfd78af_3'
+    } else {
+        container 'quay.io/biocontainers/plasmidid:1.6.4--hdfd78af_3'
+    }
+
+    input:
+    tuple val(meta), path(scaffold)
+    path  fasta
+
+    output:
+    tuple val(meta), path("${prefix}/*final_results.html"), emit: html
+    tuple val(meta), path("${prefix}/*final_results.tab") , emit: tab
+    tuple val(meta), path("${prefix}/images/")            , emit: images
+    tuple val(meta), path("${prefix}/logs/")              , emit: logs
+    tuple val(meta), path("${prefix}/data/")              , emit: data
+    tuple val(meta), path("${prefix}/database/")          , emit: database
+    tuple val(meta), path("${prefix}/fasta_files/")       , emit: fasta_files
+    tuple val(meta), path("${prefix}/kmer/")              , emit: kmer
+    path '*.version.txt'                                  , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    prefix       = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    plasmidID \\
+        -d $fasta \\
+        -s $prefix \\
+        -c $scaffold \\
+        $options.args \\
+        -o .
+
+    mv NO_GROUP/$prefix ./$prefix
+    echo \$(plasmidID --version 2>&1) > ${software}.version.txt
+    """
+}

software/plasmidid/meta.yml

@@ -0,0 +1,76 @@
+name: plasmidid
+description: assembles bacterial plasmids
+keywords:
+  - assembly
+  - plasmid
+  - bacterial
+tools:
+  - plasmidid:
+      description: Pipeline for plasmid identification and reconstruction
+      homepage: https://github.com/BU-ISCIII/plasmidID/wiki
+      documentation: https://github.com/BU-ISCIII/plasmidID#readme
+      tool_dev_url: https://github.com/BU-ISCIII/plasmidID
+      doi: ""
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - scaffold:
+      type: file
+      description: |
+        Fasta file containing scaffold
+  - fasta:
+      type: file
+      description: FASTA reference file
+      pattern: "*.{fasta,fa}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: html file with results rendered
+      pattern: "*.{html}"
+  - tab:
+      type: file
+      description: Results in a tabular file
+      pattern: "*.{tab}"
+  - images:
+      type: directory
+      description: Directory containing the images produced by plasmidid
+      pattern: "images"
+  - logs:
+      type: directory
+      description: Directory containing the logs produced by plasmidid
+      pattern: "logs"
+  - data:
+      type: directory
+      description: Directory containing the data produced by plasmidid
+      pattern: "data"
+  - database:
+      type: directory
+      description: Directory containing the database produced by plasmidid
+      pattern: "database"
+  - fasta_files:
+      type: directory
+      description: Directory containing the fasta files produced by plasmidid
+      pattern: "fasta_files"
+  - kmer:
+      type: directory
+      description: Directory containing the kmer files produced by plasmidid
+      pattern: "database"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

tests/config/pytest_software.yml

@@ -354,6 +354,10 @@ picard/mergesamfiles:
   - software/picard/mergesamfiles/**
   - tests/software/picard/mergesamfiles/**
 
+plasmidid:
+  - software/plasmidid/**
+  - tests/software/plasmidid/**
+
 preseq/lcextrap:
   - software/preseq/lcextrap/**
   - tests/software/preseq/lcextrap/**

tests/config/test_data.config

@@ -26,8 +26,11 @@ params {
 
                 test_wig_gz                               = "${test_data_dir}/genomics/sarscov2/genome/gcwiggle/test.wig.gz"
 
+                test_fas                                  = "${test_data_dir}/genomics/sarscov2/genome/alignment/test.fas"
                 all_sites_fas                             = "${test_data_dir}/genomics/sarscov2/genome/alignment/all_sites.fas"
                 informative_sites_fas                     = "${test_data_dir}/genomics/sarscov2/genome/alignment/informative_sites.fas"
+                
+                contigs_fasta                             = "${test_data_dir}/genomics/sarscov2/genome/contigs.fasta"
             }
             'illumina' {
                 test_single_end_bam                       = "${test_data_dir}/genomics/sarscov2/illumina/bam/test_single_end.bam"

tests/data/README.md

@@ -25,6 +25,7 @@ When adding a new module, please check carefully whether the data necessary for
         * 'test_genomic.dict': GATK dict for 'test_genomic.fasta'
         * 'test_genomic.fasta.fai': fasta index for 'test_genomic.fasta'
         * 'test_cds_from_genomic.fasta': coding sequencing from MT192765.1 genome (transcripts)
+        * 'contigs.fasta': contigs file obtained running Minia on sarscov2 paired-end sequencing reads files (see below)
     * fastq
         * 'test_{1,2}.fastq.gz' sarscov2 paired-end sequencing reads
         * 'test_{1,2}.2.fastq.gz‘: copies of the above reads

tests/data/genomics/sarscov2/genome/contigs.fasta

@@ -0,0 +1,26 @@
+>0 LN:i:168 KC:i:593 km:f:4.300    
+ACTCATATGAGTGTGACATACCCATTGGTGCAGGTATATGCGCTAGTTATCAGACTCAGACTAATTCTCCTCGGCGGGCACGTAGTGTAGCTAGTCAATCCATCATTGCCTACACTATGTCACTTGGTGCAGAAAATTCAGTTGCTTACTCTAATAACTCTATTGCCA
+>1 LN:i:187 KC:i:376 km:f:2.400    
+GGTCAAGGTTAATATAGGCATTAACAATGAATAATAAGAATCTACAACAGGAACTCCACTACCTGGCGTGGTTTGTATGAAATCACCGAAATCATACCAGTTACCATTGAGATCTTGATTATCTAATGTCAGTACACCAACAATACCAGCATTTCGCATGGCATCACAGAATTGTACTGTTTTTAAC
+>2 LN:i:162 KC:i:409 km:f:3.100    
+CCTAAAAAGTCTACTAATTTGGTTAAAAACAAATGTGTCAATTTCAACTTCAATGGTTTAACAGGCACAGGTGTTCTTACTGAGTCTAACAAAAAGTTTCTGCCTTTCCAACAATTTGGCAGAGACATTGCTGACACTACTGATGCTGTCCGTGATCCACAG
+>3 LN:i:207 KC:i:548 km:f:3.100    
+TCATAGATGTCAACTCAAAGCCATGTGCCCATAAGACAAATACGACTCTGTCAGAGAGATTTTTAAGTGTGTCACTTAACATTTGTACAATCTTTATACGCACTACATTCCAAGGAAGTCCTTTGTACATAAGTGGTATGAGGTGTTTAAATTGATCTCCAGGCGGTGGTTTAGCACTAACTCTGGAAAAATCTGTATTATTAGGTG
+>4 LN:i:165 KC:i:472 km:f:3.500    
+TCACCTAATTTAGCATGGCCTCTTATTGTAACAGCTTTAAGGGCCAATTCTGCTGTCAAATTACAGAATAATGAGCTTAGTCCTGTTGCACTACGACAGATGTCTTGTGCTGCCGGTACTACACAAACTGCTTGCACTGATGACAATGCGTTAGCTTACTACAAC
+>5 LN:i:174 KC:i:547 km:f:3.800    
+TCACTTTGAATTTATCAAAACACTCTACACGAGCACGTGCAGGTATAATTCTACTACATTTATCTATAGGCAAATATTTTAATGCCTTCTCACATAGTGCATCAACAGCGGCATGAGAGCAAGCTGTATACACTATGCGAGCAGAAGGGTAGTAGAGAGCTAGGCCAATAGCAA
+>6 LN:i:279 KC:i:1037 km:f:4.166    
+TAATTGCAGATGAAACATCATGCGTGATAACACCCTTATAAAACATTTTAAAGCATTGAGCTGATTTGTCTTTATGTGCTTTAAGCTTATTATCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGTGGTGCAGGTAATTGAGCAGGGTCGCCAATGTACACAT
+>7 LN:i:206 KC:i:492 km:f:2.800    
+TATATGTTTATAGTGACCACACTGGTAATTACCAGTGTACTCACTAGCACAAGTAAATGTACCATGCTTAAGTTCATACTGAGCAGGTGGTGCTGACATCATAACAAAAGGTGACTCCTGTTGTACTAGATATTTTGTAGCTTGTTTACCACACGTACAAGGTATCTGAACACCTTTCTTAAATTGTTCATAAGAAAGTGTGCCCA
+>8 LN:i:318 KC:i:1136 km:f:3.944    
+GCTTTGAGTTGACATCTATGAAGTATTTTGTGAAAATAGGACCTGAGCGCACCTGTTGTCTATGTGATAGACGTGCCACATGCTTTTCCACTGCTTCAGACACTTATGCCTGTTGGCATCATTCTATTGGATTTGATTACGTCTATAATCCGTTTATGATTGATGTTCAACAATGGGGTTTTACAGGTAACCTACAAAGCAACCATGATCTGTATTGTCAAGTCCATGGTAATGCACATGTAGCTAGTTGTGATGCAATCATGACTAGGTGTCTAGCTGTCCACGAGTGCTTTGTTAAGCGTGTTGACTGGACTATTG
+>9 LN:i:198 KC:i:386 km:f:2.300    
+ATATTGCAGCAGTACGCACACAATCGAAGCGCAGTAAGGATGGCTAGTGTAACTAGCAAGAATACCACGAAAGCAAGAAAAAGAAGTACGCTATTAACTATTAACGTACCTGTCTCTTCCGAAACGAATGAGTACATAAGTTCGTACTCATCAGCTTGTGCTTACAAAGGCACGCTAGTAGTCGTCGTCGGTTCATCA
+>10 LN:i:178 KC:i:547 km:f:3.700    
+TGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTCTAACTACTCAGGTGTAGTTACAACTGTCATGTTTTTGGCCAGAGGTATTGTTTTTATGTGTGTTGAGTATTGCCCTATTTTCTTCATAACTGGTAATACACTTCAGTGTATAATGCTAGTT
+>11 LN:i:170 KC:i:644 km:f:4.600    
+GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTGTTAAGATGTTGTGTACACACACTGGTACTGGTCAGGCA
+>12 LN:i:151 KC:i:290 km:f:2.400    
+AATTTAGTGTCAACACTGAGGTGTGTAGGTGCCTGTGTAGGATGTAACCCAGTGATTACCTTACTACAATCTTTAAAGAGTCCTGTTACATTTTCAGCTTGTAAAGTTGCCACATTCCTACGTGGAATTTCAAGACTTGTAAATTGCAACT

tests/software/plasmidid/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PLASMIDID } from '../../../software/plasmidid/main.nf' addParams ( options: ['args' : '-k 0.8'] )
+
+workflow test_plasmidid {
+
+    contigs = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['genome']['contigs_fasta'], checkIfExists: true)
+              ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    PLASMIDID ( contigs, fasta )
+}

tests/software/plasmidid/test.yml

@@ -0,0 +1,59 @@
+- name: plasmidid
+  command: nextflow run ./tests/software/plasmidid -entry test_plasmidid -c tests/config/nextflow.config
+  tags:
+    - plasmidid
+  files:
+    - path: output/plasmidid/test/data/database_reconstruct_test.length
+      md5sum: a57c401f27ae5133823fb09fb21c8a3c
+    - path: output/plasmidid/test/data/test.coverage_adapted_clustered_ac
+      md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
+    - path: output/plasmidid/test/data/test.err
+      md5sum: 1eabbbcb19d8886182f78b86fc50884c
+    - path: output/plasmidid/test/data/test.fna
+      md5sum: 78328536870d04afc54a4dfaf103cac8
+    - path: output/plasmidid/test/data/test.gbk
+      md5sum: acc40ebd7864b84fc14e5ad22e30f83f
+    - path: output/plasmidid/test/data/test.gff
+      md5sum: 0dd7015f77e2fc3ecaa978362f7334cb
+    - path: output/plasmidid/test/data/test.karyotype_individual.txt
+      md5sum: aaf0f5bfe297fb9846ace761ff018d22
+    - path: output/plasmidid/test/data/test.karyotype_summary.txt
+      md5sum: aaf0f5bfe297fb9846ace761ff018d22
+    - path: output/plasmidid/test/data/test.plasmids.blast
+      md5sum: b089b7a073f4e48fabf0949168581b4c
+    - path: output/plasmidid/test/data/test.plasmids.blast.links
+      md5sum: 3528f4e0a046826a9b7f916838b086c6
+    - path: output/plasmidid/test/data/test.plasmids.complete
+      md5sum: 8d30d205c471ee3c8151b4c3d90e753b
+    - path: output/plasmidid/test/database/test.fna
+      md5sum: 6b843fe652b4369addb382f61952c3dd
+    - path: output/plasmidid/test/database/test.gbk
+      md5sum: d2e24369b999bc6a0dae9b7612edb839
+    - path: output/plasmidid/test/database/test.gff
+      md5sum: 7e65da147d0a413020b0d92b7b03ffcd
+    - path: output/plasmidid/test/fasta_files/MT192765.1_term.fasta
+      md5sum: 2387d7d9c861e6f6e7d9f9395f9bad5c
+    - path: output/plasmidid/test/images/test_individual.circos.conf
+      md5sum: f74467ab77232e2b342e2bd408897b12
+    - path: output/plasmidid/test/images/test_MT192765.1_individual.circos.conf
+      md5sum: 548443ba0a68065a69383fe32b226780
+    - path: output/plasmidid/test/images/test_summary.circos.conf
+      md5sum: e59dc3b77ee610a48b79230da705aba0
+    - path: output/plasmidid/test/images/test_MT192765.1.png
+    - path: output/plasmidid/test/images/test_summary.png
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.clusters.tab
+      md5sum: cf75e4418631796bb4675129b575915d
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.clusters.tab
+      md5sum: cf75e4418631796bb4675129b575915d
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta
+      md5sum: 483f4a5dfe60171c86ee9b7e6dff908b
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.0.5.representative.fasta.blast.tmp.ndb
+      md5sum: f67f8be1e00eb7d3512869071fb4c2c2
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.fasta
+      md5sum: c7fe0e9e9a94d98d7f85a7be99c032fd
+    - path: output/plasmidid/test/kmer/database.filtered_0.8_term.mash.distances.tab
+      md5sum: fd5408c3c2f8f68dc01e0123bb6a9079
+    - path: output/plasmidid/test/logs/draw_circos_images.log
+    - path: output/plasmidid/test/logs/plasmidID.log
+    - path: output/plasmidid/test/test_final_results.html
+    - path: output/plasmidid/test/test_final_results.tab