Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3

modules/antismash/antismashlitedownloaddatabases/main.nf

@@ -27,9 +27,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     output:
     path("antismash_db") , emit: database
-    path("css"), emit: css_dir
-    path("detection"), emit: detection_dir
-    path("modules"), emit: modules_dir
+    path("antismash_dir"), emit: antismash_dir
     path "versions.yml", emit: versions
 
     when:
@@ -37,11 +35,19 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     script:
     def args = task.ext.args ?: ''
+    conda = params.enable_conda
     """
     download-antismash-databases \\
         --database-dir antismash_db \\
         $args
 
+    if [[ $conda = false ]]; \
+        then \
+            cp -r /usr/local/lib/python3.8/site-packages/antismash antismash_dir; \
+        else \
+            cp -r \$(python -c 'import antismash;print(antismash.__file__.split("/__")[0])') antismash_dir; \
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         antismash-lite: \$(antismash --version | sed 's/antiSMASH //')

modules/antismash/antismashlitedownloaddatabases/meta.yml

@@ -50,21 +50,11 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
-  - css_dir:
+  - antismash_dir:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "css"
-  - detection_dir:
-      type: directory
-      description: |
-        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "detection"
-  - modules_dir:
-      type: directory
-      description: |
-        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
-      pattern: "modules"
+        antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines.
+      pattern: "antismash_dir"
 
 authors:
   - "@jasmezz"

modules/srst2/srst2/main.nf

@@ -0,0 +1,47 @@
+process SRST2_SRST2 {
+    tag "${meta.id}"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::srst2=0.2.0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/srst2%3A0.2.0--py27_2':
+        'quay.io/biocontainers/srst2:0.2.0--py27_2'}"
+
+    input:
+    tuple val(meta), path(fastq_s), path(db)
+
+    output:
+    tuple val(meta), path("*_genes_*_results.txt")               , optional:true, emit: gene_results
+    tuple val(meta), path("*_fullgenes_*_results.txt")           , optional:true, emit: fullgene_results
+    tuple val(meta), path("*_mlst_*_results.txt")                , optional:true, emit: mlst_results
+    tuple val(meta), path("*.pileup")                            ,                emit: pileup
+    tuple val(meta), path("*.sorted.bam")                        ,                emit: sorted_bam
+    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}"
+    def read_s = meta.single_end ? "--input_se ${fastq_s}" : "--input_pe ${fastq_s[0]} ${fastq_s[1]}"
+    if (meta.db=="gene") {
+        database = "--gene_db ${db}"
+    } else if (meta.db=="mlst") {
+        database = "--mlst_db ${db}"
+    } else {
+        error "Please set meta.db to either \"gene\" or \"mlst\""
+    }
+    """
+    srst2 \\
+        ${read_s} \\
+        --threads $task.cpus \\
+        --output ${prefix} \\
+        ${database} \\
+        $args
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        srst2: \$(echo \$(srst2 --version 2>&1) | sed 's/srst2 //' ))
+    END_VERSIONS
+    """
+}

modules/srst2/srst2/meta.yml

@@ -0,0 +1,72 @@
+name: srst2_srst2
+description: |
+  Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,
+  a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)
+  and report the presence of STs and/or reference genes.
+keywords:
+  - mlst
+  - typing
+  - illumina
+tools:
+  - srst2:
+      description: "Short Read Sequence Typing for Bacterial Pathogens"
+      homepage: "http://katholt.github.io/srst2/"
+      documentation: "https://github.com/katholt/srst2/blob/master/README.md"
+      tool_dev_url: "https://github.com/katholt/srst2"
+      doi: "10.1186/s13073-014-0090-6"
+      licence: ["BSD"]
+
+input:
+  - meta:
+      type: map0.2.0-4
+      description: |
+        Groovy Map containing sample information
+        id: should be the identification number or sample name
+        single_end: should be true for single end data and false for paired in data
+        db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option
+        e.g. [ id:'sample', single_end:false , db:'gene']
+  - fasta:
+      type: file
+      description: |
+        gzipped fasta file. If files are NOT in
+        MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise
+        default is _1, i.e. expect forward reads as sample_1.fastq.gz).
+      pattern: "*.fastq.gz"
+  - db:
+      type: file
+      description: Database in FASTA format
+      pattern: "*.fasta"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'sample', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - txt:
+      type: file
+      description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
+      pattern: "*_fullgenes_*_results.txt"
+  - txt:
+      type: file
+      description: A tabulated summary report of samples x genes.
+      pattern: "*_genes_*_results.txt"
+  - txt:
+      type: file
+      description: A tabulated summary report of mlst subtyping.
+      pattern: "*_mlst_*_results.txt"
+  - bam:
+      type: file
+      description: Sorted BAM file
+      pattern: "*.sorted.bam"
+  - pileup:
+      type: file
+      description: SAMtools pileup file
+      pattern: "*.pileup"
+
+authors:
+  - "@jvhagey"

tests/config/pytest_modules.yml

@@ -1775,6 +1775,10 @@ sratools/prefetch:
   - modules/sratools/prefetch/**
   - tests/modules/sratools/prefetch/**
 
+srst2/srst2:
+  - modules/srst2/srst2/**
+  - tests/modules/srst2/srst2/**
+
 ssuissero:
   - modules/ssuissero/**
   - tests/modules/ssuissero/**

tests/modules/antismash/antismashlitedownloaddatabases/test.yml

@@ -1,8 +1,8 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash
     - antismash/antismashlitedownloaddatabases
+    - antismash
   files:
     - path: output/antismash/versions.yml
       md5sum: 24859c67023abab99de295d3675a24b6
@@ -12,6 +12,5 @@
     - path: output/antismash/antismash_db/pfam
     - path: output/antismash/antismash_db/resfam
     - path: output/antismash/antismash_db/tigrfam
-    - path: output/antismash/css
-    - path: output/antismash/detection
-    - path: output/antismash/modules
+    - path: output/antismash/antismash_dir
+    - path: output/antismash/antismash_dir/detection/hmm_detection/data/bgc_seeds.hmm

tests/modules/srst2/srst2/main.nf

@@ -0,0 +1,53 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRST2_SRST2 } from '../../../../modules/srst2/srst2/main.nf'
+
+workflow test_srst2_srst2_exit {
+
+    input = [
+        [ id:'test', single_end:false, db:"test"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+//        [("")]
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_mlst {
+
+    input = [
+        [ id:'test', single_end:false, db:"mlst"], // meta map
+        [ file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_1.fastq.gz", checkIfExists: true),
+          file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/SRR9067271_2.fastq.gz", checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/MLST_DB.fas')
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_paired_end {
+
+    input = [
+        [ id:'test', single_end:false, db:"gene"], // meta map
+        [ file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+          file(params.test_data['bacteroides_fragilis']['illumina']['test1_2_fastq_gz'], checkIfExists: true) ],
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}
+
+workflow test_srst2_srst2_single_end {
+
+    input = [
+        [ id:'test', single_end:true, db:"gene" ], // meta map
+        file(params.test_data['bacteroides_fragilis']['illumina']['test1_1_fastq_gz'], checkIfExists: true),
+        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/srst2/resFinder_20180221_srst2.fasta')  // Change to params.test_data syntax after the data is included in tests/config/test_data.config
+    ]
+
+    SRST2_SRST2(input)
+}

tests/modules/srst2/srst2/nextflow.config

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

tests/modules/srst2/srst2/test.yml

@@ -0,0 +1,51 @@
+- name: srst2 srst2 test_srst2_srst2_exit #Testing pipeline exit when not meta.db
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_exit -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  exit_code: 1
+
+- name: srst2 srst2 test_srst2_srst2_mlst
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_mlst -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__SRR9067271.MLST_DB.pileup
+      contains:
+        - "dnaJ-1	2	C	17	.........,.......	FFFFFFFFFFFFFFFFF"
+    - path: output/srst2/test__SRR9067271.MLST_DB.sorted.bam
+    - path: output/srst2/test__mlst__MLST_DB__results.txt
+      md5sum: ec1b1f69933401d67c57f64cad11a098
+    - path: output/srst2/versions.yml
+      md5sum: a0c256a2fd3636069710b8ef22ee5ea7
+
+- name: srst2 srst2 test_srst2_srst2_paired_end
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_paired_end -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: 099aa6cacec5524b311f606debdfb3a9
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.pileup
+      md5sum: 64b512ff495b828c456405ec7b676ad1
+    - path: output/srst2/test__test1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: b446a70f1a2b4f60757829bcd744a214
+
+- name: srst2 srst2 test_srst2_srst2_single_end
+  command: nextflow run tests/modules/srst2/srst2 -entry test_srst2_srst2_single_end -c tests/config/nextflow.config
+  tags:
+    - srst2/srst2
+    - srst2
+  files:
+    - path: output/srst2/test__fullgenes__resFinder_20180221_srst2__results.txt
+      md5sum: d0762ef8c38afd0e0a34cce52ed1a3db
+    - path: output/srst2/test__genes__resFinder_20180221_srst2__results.txt
+      md5sum: b8850c6644406d8b131e471ecc3f9013
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.pileup
+      md5sum: 5f6279dc8124aa762a9dfe3d7a871277
+    - path: output/srst2/test__test1_1.resFinder_20180221_srst2.sorted.bam
+    - path: output/srst2/versions.yml
+      md5sum: 790fe00493c6634d17801a930073218b