Linting upgrade

.editorconfig

@@ -10,3 +10,11 @@ indent_style = space
 
 [*.{md,yml,yaml,cff}]
 indent_size = 2
+
+[*.{cm,dmnd}]
+charset = utf-8
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_size = unset
+indent_style = unset

modules/ebi-metagenomics/blastp/main.nf → modules/ebi-metagenomics/blast/blastp/main.nf

@@ -1,5 +1,5 @@
 // currently outputs the CSV only with outfmt = 10
-process BLASTP {
+process BLAST_BLASTP {
     tag "$meta.id"
     label 'process_medium'
 

modules/ebi-metagenomics/blastp/meta.yml → modules/ebi-metagenomics/blast/blastp/meta.yml

@@ -1,13 +1,13 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
-name: "blastp"
+name: "blast_blastp"
 description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database
 keywords:
   - protein alignment
   - functional annotation
   - evolutionary analysis
 tools:
-  - "blastp":
+  - "blast_blastp":
       description: "BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database"
       homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
       documentation: "https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs"

modules/ebi-metagenomics/blast/makeblastdb/main.nf

@@ -0,0 +1,33 @@
+process BLAST_MAKEBLASTDB {
+    tag "$fasta"
+    label 'process_medium'
+
+    conda "bioconda::blast=2.13.0"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
+        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
+
+    input:
+    path fasta
+
+    output:
+    path 'blast_db'     , emit: db
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    makeblastdb \\
+        -in $fasta \\
+        $args
+    mkdir blast_db
+    mv ${fasta}* blast_db
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/blast/makeblastdb/meta.yml

@@ -0,0 +1,31 @@
+name: blast_makeblastdb
+description: Builds a BLAST database
+keywords:
+  - fasta
+  - blast
+  - database
+tools:
+  - blast:
+      description: |
+        BLAST finds regions of similarity between biological sequences.
+      homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi
+      documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs
+      doi: 10.1016/S0022-2836(05)80360-2
+      licence: ["US-Government-Work"]
+input:
+  - fasta:
+      type: file
+      description: Input fasta file
+      pattern: "*.{fa,fasta}"
+output:
+  - db:
+      type: directory
+      description: Output directory containing blast database files
+      pattern: "*"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@joseespinosa"
+  - "@drpatelh"

modules/ebi-metagenomics/bmtagger/bmtagger/main.nf

@@ -1,9 +1,11 @@
-process BMTAGGER {
+process BMTAGGER_BMTAGGER {
 
     tag "$meta.id"
 
     label 'process_low'
 
+    debug true
+
     conda "bioconda::bmtagger=3.101"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bmtagger:3.101--h470a237_4':
@@ -17,8 +19,8 @@ process BMTAGGER {
     val output_file
 
     output:
-    tuple val(meta), path("${output_file}")          , emit: output_host
-    path "versions.yml"                              , emit: versions
+    tuple val(meta), path("${output_file}"), emit: output_host
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,7 +34,7 @@ process BMTAGGER {
     } else if (input_format == 'fastq') {
         args += ' -q1 '
     } else {
-        print('unknown format')
+        error "Invalid format: ${input_format}"
     }
 
     if (meta.single_end) {
@@ -65,7 +67,7 @@ process BMTAGGER {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        bmtagger: \$(bmtagger.sh -hV | grep 'version' )
+        bmtagger: \$(bmtagger.sh -hV 2>1 | grep version | grep -Eo '[0-9.]+')
     END_VERSIONS
     """
 }

modules/ebi-metagenomics/bmtagger/bmtagger/meta.yml

@@ -1,12 +1,12 @@
 ---
-name: "bmtagger"
+name: "bmtagger_bmtagger"
 description: Bmtagger tools
 keywords:
   - decontamination
   - host
   - reference_genome
 tools:
-  - "bmtagger":
+  - "bmtagger_bmtagger":
       description: "Best Match Tagger for removing human reads from metagenomics datasets"
       homepage: "https://bioconda-recipes-demo.readthedocs.io/en/docs/recipes/bmtagger/README.html"
       documentation: "https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/README.bmtagger.txt"
@@ -19,7 +19,7 @@ input:
         e.g. `[ id:'test', single_end:false ]`
 
   - input:
-      type: list
+      type: file
       description: fasta or fastq files
       pattern: "*.{fa,fq,fasta,fastq}"
 

modules/ebi-metagenomics/bmtagger/indexreference/main.nf

@@ -0,0 +1,67 @@
+process BMTAGGER_INDEXREFERENCE {
+    tag "${reference_fasta}"
+    label 'process_low'
+
+    conda "bioconda::bmtagger=3.101"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bmtagger:3.101--h470a237_4':
+        'biocontainers/bmtagger:3.101--h470a237_4' }"
+
+    input:
+    path(reference_fasta)
+
+    output:
+    path("${reference_fasta.simpleName}.bitmask")  , emit: bitmask
+    path("${reference_fasta.simpleName}.srprism.*"), emit: srprism
+    path("${reference_fasta.simpleName}.n*")       , emit: blast_db
+    path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args_bmtool = task.ext.args_bmtool ?: '-A 0 -w 18'
+    def args_srprism = task.ext.args_srprism ?: '-M 7168'
+    def args_makeblastdb = task.ext.args_makeblastdb ?: '-dbtype nucl'
+    """
+    bmtool -d ${reference_fasta} -o ${reference_fasta.simpleName}.bitmask ${args_bmtool}
+    srprism mkindex -i ${reference_fasta} -o ${reference_fasta.simpleName}.srprism ${args_srprism}
+    makeblastdb -in ${reference_fasta} ${args_makeblastdb}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bmtool: \$(bmtool --version | tr ' ' '\\t' | cut -f2)
+        srprism: \$(srprism 2>&1 | grep version | sed 's/^.*version //; s/ .*\$//')
+        makeblastdb: \$(makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch ${reference_fasta.simpleName}.bitmask
+    touch ${reference_fasta.simpleName}.srprism.idx
+    touch ${reference_fasta.simpleName}.srprism.amp
+    touch ${reference_fasta.simpleName}.srprism.idx
+    touch ${reference_fasta.simpleName}.srprism.imp
+    touch ${reference_fasta.simpleName}.srprism.map
+    touch ${reference_fasta.simpleName}.srprism.pmp
+    touch ${reference_fasta.simpleName}.srprism.rmp
+    touch ${reference_fasta.simpleName}.srprism.ss
+    touch ${reference_fasta.simpleName}.srprism.ssa
+    touch ${reference_fasta.simpleName}.srprism.ssd
+    touch ${reference_fasta.simpleName}.nsq
+    touch ${reference_fasta.simpleName}.nhr
+    touch ${reference_fasta.simpleName}.nhr
+    touch ${reference_fasta.simpleName}.nin
+    touch ${reference_fasta.simpleName}.nin
+    touch ${reference_fasta.simpleName}.nsq
+    touch ${reference_fasta.simpleName}.nsq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bmtool: \$(bmtool --version | tr ' ' '\\t' | cut -f2)
+        srprism: \$(srprism 2>&1 | grep version | sed 's/^.*version //; s/ .*\$//')
+        makeblastdb: \$(makeblastdb -version 2>&1 | sed 's/^.*makeblastdb: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/ebi-metagenomics/bmtagger/index_reference/main.yml → modules/ebi-metagenomics/bmtagger/indexreference/meta.yml

@@ -1,9 +1,11 @@
 ---
-name: "index_reference"
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "bmtagger_indexreference"
 description: Create indexed reference DB for bmtagger
 keywords:
   - reference
   - index
+  - fasta
 tools:
   - "bmtool":
       description: "Tool from bmtagger to create a bitmask file for the reference genome"
@@ -15,7 +17,7 @@ tools:
       documentation: "https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/README.bmtagger.txt"
   - "makeblastdb":
       description: "Tool from blast to index reference genome"
-      homepage: " ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/"
+      homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
 
 input:
   - reference_fasta:
@@ -46,3 +48,4 @@ output:
 
 authors:
   - "@KateSakharova"
+  - "@vagkaratzas"

modules/ebi-metagenomics/combinedgenecaller/merge/Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.9-slim
+
+WORKDIR /combined_gene_caller
+
+COPY . .
+
+RUN pip install --no-cache .
+
+CMD [ "combined_gene_caller" ]

modules/ebi-metagenomics/fetchtool/assembly/Dockerfile

@@ -0,0 +1,21 @@
+FROM python:3.9-slim
+
+LABEL maintainer="Microbiome Informatics"
+LABEL version="0.9.0"
+LABEL description="EBI Fetch Tool Docker Image."
+
+# We need curl to download aspera and ps for nextflow monitoring
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt update && apt install -y curl procps && rm -rf /var/lib/apt/lists/*
+
+COPY . .
+
+RUN pip install --no-cache-dir .
+
+# Aspera is an IBM library for data sharing
+RUN ./install-aspera.sh
+
+RUN export PATH=$PATH:/aspera-cli/cli/bin
+
+CMD [ fetch-read-tool ]

modules/ebi-metagenomics/prodigal/main.nf

@@ -1,6 +1,3 @@
-// This module is a verbatim copy of https://github.com/nf-core/modules/blob/master/modules/nf-core/prodigal/main.nf
-// I've copied this as I still have to figure out how to handle nf-core/subworkflows that have dependencies from > 1
-// nf-core repo.
 process PRODIGAL {
     tag "$meta.id"
     label 'process_single'

subworkflows/ebi-metagenomics/combined_gene_caller/main.nf

@@ -45,4 +45,3 @@ workflow COMBINED_GENE_CALLER {
     ffn      = COMBINEDGENECALLER_MERGE.out.ffn  // channel: [ val(meta), [ ffn ] ]
     versions = ch_versions                       // channel: [ versions.yml ]
 }
-

tests/config/pytest_modules.yml

@@ -1,11 +1,19 @@
-blastp:
-  - modules/ebi-metagenomics/blastp/**
-  - tests/modules/ebi-metagenomics/blastp/**
+blast/makeblastdb:
+  - modules/ebi-metagenomics/blast/makeblastdb/**
+  - tests/modules/ebi-metagenomics/blast/makeblastdb/**
+
+blast/blastp:
+  - modules/ebi-metagenomics/blast/blastp/**
+  - tests/modules/ebi-metagenomics/blast/blastp/**
 
 bmtagger/bmtagger:
   - modules/ebi-metagenomics/bmtagger/bmtagger/**
   - tests/modules/ebi-metagenomics/bmtagger/bmtagger/**
 
+bmtagger/indexreference:
+  - modules/ebi-metagenomics/bmtagger/indexreference/**
+  - tests/modules/ebi-metagenomics/bmtagger/indexreference/**
+
 cmsearchtbloutdeoverlap:
   - modules/ebi-metagenomics/cmsearchtbloutdeoverlap/**
   - tests/modules/ebi-metagenomics/cmsearchtbloutdeoverlap/**
@@ -34,6 +42,10 @@ infernal/cmsearch:
   - modules/ebi-metagenomics/infernal/cmsearch/**
   - tests/modules/ebi-metagenomics/infernal/cmsearch/**
 
+prodigal:
+  - modules/ebi-metagenomics/prodigal/**
+  - tests/modules/ebi-metagenomics/prodigal/**
+
 seqtk/seq:
   - modules/ebi-metagenomics/seqtk/seq/**
   - tests/modules/ebi-metagenomics/seqtk/seq/**