Merge branch 'master' into add_compression_to_bam2fq

modules/shigatyper/main.nf

@@ -0,0 +1,64 @@
+process SHIGATYPER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::shigatyper=2.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/shigatyper%3A2.0.1--pyhdfd78af_0':
+        'quay.io/biocontainers/shigatyper:2.0.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("${prefix}.tsv")     , emit: tsv
+    tuple val(meta), path("${prefix}-hits.tsv"), optional: true, emit: hits
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    if (meta.is_ont) {
+        """
+        shigatyper \\
+            $args \\
+            --SE $reads \\
+            --ont \\
+            --name $prefix
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
+        END_VERSIONS
+        """
+    } else if (meta.single_end) {
+        """
+        shigatyper \\
+            $args \\
+            --SE $reads \\
+            --name $prefix
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
+        END_VERSIONS
+        """
+    } else {
+        """
+        shigatyper \\
+            $args \\
+            --R1 ${reads[0]} \\
+            --R2 ${reads[1]} \\
+            --name $prefix
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            shigatyper: \$(echo \$(shigatyper --version 2>&1) | sed 's/^.*ShigaTyper //' )
+        END_VERSIONS
+        """
+    }
+}

modules/shigatyper/meta.yml

@@ -0,0 +1,47 @@
+name: "shigatyper"
+description: Determine Shigella serotype from Illumina or Oxford Nanopore reads
+keywords:
+  - fastq
+  - shigella
+  - serotype
+tools:
+  - "shigatyper":
+      description: "Typing tool for Shigella spp. from WGS Illumina sequencing"
+      homepage: "https://github.com/CFSAN-Biostatistics/shigatyper"
+      documentation: "https://github.com/CFSAN-Biostatistics/shigatyper"
+      tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper"
+      doi: "10.1128/AEM.00165-19"
+      licence: "['Public Domain']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false, is_ont:false ]
+  - reads:
+      type: file
+      description: Illumina or Nanopore FASTQ file
+      pattern: "*.fastq.gz"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - tsv:
+      type: file
+      description: A TSV formatted file with ShigaTyper results
+      pattern: "*.tsv"
+  - hits:
+      type: file
+      description: A TSV formatted file with individual gene hits
+      pattern: "*-hits.tsv"
+
+authors:
+  - "@rpetit3"

modules/slimfastq/main.nf

@@ -0,0 +1,52 @@
+def VERSION = '2.04'
+
+process SLIMFASTQ {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2':
+        'quay.io/biocontainers/slimfastq:2.04--h87f3376_2' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.sfq"), emit: sfq
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if (meta.single_end) {
+        """
+        gzip -d -c '${fastq}' | slimfastq \\
+            $args \\
+            -f '${prefix}.sfq'
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            slimfastq: ${VERSION}
+        END_VERSIONS
+        """
+    } else {
+        """
+        gzip -d -c '${fastq[0]}' | slimfastq \\
+            $args \\
+            -f '${prefix}_1.sfq'
+
+        gzip -d -c '${fastq[1]}' | slimfastq \\
+            $args \\
+            -f '${prefix}_2.sfq'
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            slimfastq: ${VERSION}
+        END_VERSIONS
+        """
+    }
+}

modules/slimfastq/meta.yml

@@ -0,0 +1,41 @@
+name: "slimfastq"
+description: Fast, efficient, lossless compression of FASTQ files.
+keywords:
+  - FASTQ
+  - compression
+  - lossless
+tools:
+  - "slimfastq":
+      description: "slimfastq efficiently compresses/decompresses FASTQ files"
+      homepage: "https://github.com/Infinidat/slimfastq"
+      tool_dev_url: "https://github.com/Infinidat/slimfastq"
+      licence: "['BSD-3-clause']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: Either a single-end FASTQ file or paired-end files.
+      pattern: "*.{fq.gz,fastq.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - sfq:
+      type: file
+      description: Either one or two sequence files in slimfastq compressed format.
+      pattern: "*.{sfq}"
+
+authors:
+  - "@Midnighter"

tests/config/pytest_modules.yml

@@ -1719,6 +1719,10 @@ seqwish/induce:
   - modules/seqwish/induce/**
   - tests/modules/seqwish/induce/**
 
+shigatyper:
+  - modules/shigatyper/**
+  - tests/modules/shigatyper/**
+
 shovill:
   - modules/shovill/**
   - tests/modules/shovill/**
@@ -1727,6 +1731,10 @@ sistr:
   - modules/sistr/**
   - tests/modules/sistr/**
 
+slimfastq:
+  - modules/slimfastq/**
+  - tests/modules/slimfastq/**
+
 snapaligner/index:
   - modules/snapaligner/index/**
   - tests/modules/snapaligner/index/**

tests/modules/shigatyper/main.nf

@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SHIGATYPER } from '../../../modules/shigatyper/main.nf'
+
+workflow test_shigatyper_pe {
+    
+    input = [ 
+        [ id:'test', single_end:false, is_ont:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}
+
+workflow test_shigatyper_se {
+    
+    input = [ 
+        [ id:'test', single_end:true, is_ont:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}
+
+workflow test_shigatyper_ont {
+    
+    input = [ 
+        [ id:'test', single_end:true, is_ont:true ], // meta map
+        [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
+    ]
+
+    SHIGATYPER ( input )
+}

tests/modules/shigatyper/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/shigatyper/test.yml

@@ -0,0 +1,29 @@
+- name: shigatyper test_shigatyper_pe
+  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_pe -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: d8ca45ed88dfba9bc570c01e4b49773b
+
+- name: shigatyper test_shigatyper_se
+  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_se -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: 8bbf165da5a5df3b7771a33aad197eec
+
+- name: shigatyper test_shigatyper_ont
+  command: nextflow run tests/modules/shigatyper -entry test_shigatyper_ont -c tests/config/nextflow.config -c tests/modules/shigatyper/nextflow.config
+  tags:
+    - shigatyper
+  files:
+    - path: output/shigatyper/test.tsv
+      md5sum: 4f7d38c956993800546b9acb9881d717
+    - path: output/shigatyper/versions.yml
+      md5sum: 0da333e1178e9e7e84a9116ad5a5ff71

tests/modules/slimfastq/main.nf

@@ -0,0 +1,46 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SLIMFASTQ } from '../../../modules/slimfastq/main.nf'
+
+workflow test_slimfastq_single_end {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_paired_end {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+         file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_nanopore {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}
+
+workflow test_slimfastq_pacbio {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['homo_sapiens']['pacbio']['ccs_fq_gz'], checkIfExists: true)
+    ]
+
+    SLIMFASTQ ( input )
+}

tests/modules/slimfastq/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/slimfastq/test.yml

@@ -0,0 +1,41 @@
+- name: slimfastq test_slimfastq_single_end
+  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_single_end -c tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
+    - path: output/slimfastq/versions.yml
+      md5sum: f52351f5c9e6259af02745c8eae5c780
+
+- name: slimfastq test_slimfastq_paired_end
+  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_paired_end -c tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test_1.sfq
+      md5sum: 6a942eeca6c99ee9a9a0cedab5d246f1
+    - path: output/slimfastq/test_2.sfq
+      md5sum: 0d2c60b52a39f7c2cb7843e848d90afd
+    - path: output/slimfastq/versions.yml
+      md5sum: 6239853705877651a4851c4cb6d62da4
+
+- name: slimfastq test_slimfastq_nanopore
+  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_nanopore -c tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: e17f14d64d3a75356b03ff2f9e8881f7
+    - path: output/slimfastq/versions.yml
+      md5sum: 33153f1103482a2bd35cb2f4c337c5e8
+
+- name: slimfastq test_slimfastq_pacbio
+  command: nextflow run tests/modules/slimfastq -entry test_slimfastq_pacbio -c tests/config/nextflow.config
+  tags:
+    - slimfastq
+  files:
+    - path: output/slimfastq/test.sfq
+      md5sum: 9e8389e47e6ddf8c25e92412dd628339
+    - path: output/slimfastq/versions.yml
+      md5sum: 1982789c3d5c7de37c0a9351e4ae63f7