Merge branch 'nf-core:master' into master

modules/bamtools/convert/main.nf

@@ -0,0 +1,38 @@
+process BAMTOOLS_CONVERT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
+        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
+    path "versions.yml"                                              , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
+    if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
+    m = args =~ /-format ([a-z]+)/
+    ext = m[0][1]
+
+
+    """
+    bamtools \\
+        convert \\
+        $args \\
+        -in $bam \\
+        -out ${prefix}.${ext}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
+    END_VERSIONS
+    """
+}

modules/bamtools/convert/meta.yml

@@ -0,0 +1,52 @@
+name: bamtools_convert
+description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
+keywords:
+  - bamtools
+  - bamtools/convert
+  - bam
+  - convert
+  - bed
+  - fasta
+  - fastq
+  - json
+  - pileup
+  - sam
+  - yaml
+tools:
+  - bamtools:
+      description: C++ API & command-line toolkit for working with BAM data
+      homepage: http://github.com/pezmaster31/bamtools
+      documentation: https://github.com/pezmaster31/bamtools/wiki
+      tool_dev_url: http://github.com/pezmaster31/bamtools
+      doi: ""
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.bam"
+
+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"
+  ## TODO nf-core: Delete / customise this example output
+  - out:
+      type: file
+      description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml)
+      pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}"
+
+authors:
+  - "@sguizard"

modules/freebayes/main.nf

@@ -41,7 +41,7 @@ process FREEBAYES {
             $args \\
             $input > ${prefix}.vcf
 
-        gzip --no-name ${prefix}.vcf
+        bgzip ${prefix}.vcf
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -60,7 +60,7 @@ process FREEBAYES {
             $args \\
             $input > ${prefix}.vcf
 
-        gzip --no-name ${prefix}.vcf
+        bgzip ${prefix}.vcf
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":

modules/gatk4/mergebamalignment/main.nf

@@ -8,8 +8,7 @@ process GATK4_MERGEBAMALIGNMENT {
         'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(aligned)
+    tuple val(meta), path(aligned), path(unmapped)
-    path  unmapped
     path  fasta
     path  dict
 
@@ -28,10 +27,10 @@ process GATK4_MERGEBAMALIGNMENT {
     }
     """
     gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
-        ALIGNED=$aligned \\
+        -ALIGNED $aligned \\
-        UNMAPPED=$unmapped \\
+        -UNMAPPED $unmapped \\
-        R=$fasta \\
+        -R $fasta \\
-        O=${prefix}.bam \\
+        -O ${prefix}.bam \\
         $args
 
     cat <<-END_VERSIONS > versions.yml

modules/nextclade/datasetget/main.nf

@@ -2,10 +2,10 @@ process NEXTCLADE_DATASETGET {
     tag "$dataset"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
 
     input:
     val dataset

modules/nextclade/run/main.nf

@@ -2,10 +2,10 @@ process NEXTCLADE_RUN {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::nextclade=1.9.0" : null)
+    conda (params.enable_conda ? "bioconda::nextclade=1.10.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/nextclade:1.9.0--h9ee0642_0' :
+        'https://depot.galaxyproject.org/singularity/nextclade:1.10.1--h9ee0642_0' :
-        'quay.io/biocontainers/nextclade:1.9.0--h9ee0642_0' }"
+        'quay.io/biocontainers/nextclade:1.10.1--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fasta)

modules/prodigal/main.nf

@@ -2,27 +2,27 @@ process PRODIGAL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::prodigal=2.6.3" : null)
+    conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/prodigal:2.6.3--h516909a_2' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
-        'quay.io/biocontainers/prodigal:2.6.3--h516909a_2' }"
+        'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
 
     input:
     tuple val(meta), path(genome)
     val(output_format)
 
     output:
-    tuple val(meta), path("${prefix}.${output_format}"), emit: gene_annotations
+    tuple val(meta), path("${prefix}.${output_format}"),    emit: gene_annotations
-    tuple val(meta), path("${prefix}.fna"), emit: nucleotide_fasta
+    tuple val(meta), path("${prefix}.fna"),                 emit: nucleotide_fasta
-    tuple val(meta), path("${prefix}.faa"), emit: amino_acid_fasta
+    tuple val(meta), path("${prefix}.faa"),                 emit: amino_acid_fasta
-    tuple val(meta), path("${prefix}_all.txt"), emit: all_gene_annotations
+    tuple val(meta), path("${prefix}_all.txt"),             emit: all_gene_annotations
-    path "versions.yml"           , emit: versions
+    path "versions.yml",                                    emit: versions
 
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
     """
-    prodigal -i "${genome}" \\
+    pigz -cdf ${genome} | prodigal \\
         $args \\
         -f $output_format \\
         -d "${prefix}.fna" \\
@@ -33,6 +33,7 @@ process PRODIGAL {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
+        pigz: \$(pigz -V 2>&1 | sed 's/pigz //g')
     END_VERSIONS
     """
 }

modules/prodigal/meta.yml

@@ -5,10 +5,10 @@ keywords:
 tools:
   - prodigal:
       description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
-      homepage: {}
+      homepage: {https://github.com/hyattpd/Prodigal}
-      documentation: {}
+      documentation: {https://github.com/hyattpd/prodigal/wiki}
       tool_dev_url: {}
-      doi: ""
+      doi: "10.1186/1471-2105-11-119"
       licence: ["GPL v3"]
 
 input:
@@ -17,10 +17,12 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - bam:
+  - genome:
       type: file
-      description: BAM/CRAM/SAM file
+      description: fasta/fasta.gz file
-      pattern: "*.{bam,cram,sam}"
+  - output_format:
+      type: string
+      description: Output format ("gbk"/"gff"/"sqn"/"sco")
 
 output:
   - meta:
@@ -32,10 +34,22 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - bam:
+  - nucleotide_fasta:
       type: file
-      description: Sorted BAM/CRAM/SAM file
+      description: nucleotide sequences file
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.{fna}"
+  - amino_acid_fasta:
+      type: file
+      description: protein translations file
+      pattern: "*.{faa}"
+  - all_gene_annotations:
+      type: file
+      description: complete starts file
+      pattern: "*.{_all.txt}"
+  - gene_annotations:
+      type: file
+      description: gene annotations in output_format given as input
+      pattern: "*.{output_format}"
 
 authors:
   - "@grst"

tests/config/pytest_modules.yml

@@ -46,6 +46,10 @@ bamaligncleaner:
   - modules/bamaligncleaner/**
   - tests/modules/bamaligncleaner/**
 
+bamtools/convert:
+  - modules/bamtools/convert/**
+  - tests/modules/bamtools/convert/**
+
 bamtools/split:
   - modules/bamtools/split/**
   - tests/modules/bamtools/split/**

tests/modules/bamtools/convert/main.nf

@@ -0,0 +1,104 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_EXT_ERROR }   from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_NOEXT_ERROR } from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_BED }         from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTA }       from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_FASTQ }       from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_JSON }        from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_PILEUP }      from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_SAM }         from '../../../../modules/bamtools/convert/main.nf'
+include { BAMTOOLS_CONVERT as BAMTOOLS_CONVERT_YAML }        from '../../../../modules/bamtools/convert/main.nf'
+
+workflow test_bamtools_convert_ext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_EXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_noext_error {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_NOEXT_ERROR ( input )
+}
+
+workflow test_bamtools_convert_bed {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_BED ( input )
+}
+
+workflow test_bamtools_convert_fasta {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTA ( input )
+}
+
+workflow test_bamtools_convert_fastq {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_FASTQ ( input )
+}
+
+workflow test_bamtools_convert_json {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_JSON ( input )
+}
+
+workflow test_bamtools_convert_pileup {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_PILEUP ( input )
+}
+
+workflow test_bamtools_convert_sam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_SAM ( input )
+}
+
+workflow test_bamtools_convert_yaml {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    BAMTOOLS_CONVERT_YAML ( input )
+}
+

tests/modules/bamtools/convert/nextflow.config

@@ -0,0 +1,41 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: BAMTOOLS_CONVERT_EXT_ERROR {
+        ext.args = "-format vcf"
+    }
+
+    withName: BAMTOOLS_CONVERT_NOEXT_ERROR {
+        ext.args = ""
+    }
+
+    withName: BAMTOOLS_CONVERT_BED {
+        ext.args = "-format bed"
+    }
+
+    withName: BAMTOOLS_CONVERT_FASTA {
+        ext.args = "-format fasta"
+    }
+
+    withName: BAMTOOLS_CONVERT_FASTQ {
+        ext.args = "-format fastq"
+    }
+
+    withName: BAMTOOLS_CONVERT_JSON {
+        ext.args = "-format json"
+    }
+
+    withName: BAMTOOLS_CONVERT_PILEUP {
+        ext.args = "-format pileup"
+    }
+
+    withName: BAMTOOLS_CONVERT_SAM {
+        ext.args = "-format sam"
+    }
+
+    withName: BAMTOOLS_CONVERT_YAML {
+        ext.args = "-format yaml"
+    }
+
+}

tests/modules/bamtools/convert/test.yml

@@ -0,0 +1,90 @@
+- name: bamtools convert test_bamtools_convert_ext_error
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_ext_error -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_noext_error
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_noext_error -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  exit_code: 1
+
+- name: bamtools convert test_bamtools_convert_bed
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_bed -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.bed
+      md5sum: 4e34cc15bf31e700f5f3a9f8fffb6c81
+    - path: output/bamtools/versions.yml
+      md5sum: eb7a144b8a97965d3482f6f96b8a8243
+
+- name: bamtools convert test_bamtools_convert_fasta
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fasta -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fasta
+      md5sum: 52aeacf78571862b7e97c7d44ac8f827
+    - path: output/bamtools/versions.yml
+      md5sum: 42d19a2b2b07f05edb82b34369dfd754
+
+- name: bamtools convert test_bamtools_convert_fastq
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_fastq -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.fastq
+      md5sum: e591c48daad2c56638e5d6f21f1f71c5
+    - path: output/bamtools/versions.yml
+      md5sum: 13f0bf8a3e1f8f527f96dabaa5c8051e
+
+- name: bamtools convert test_bamtools_convert_json
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_json -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.json
+      md5sum: 04afed696f9f14da85a460353645d1f5
+    - path: output/bamtools/versions.yml
+      md5sum: 33d633dbd6209cb93c9b071f8c0ed3b3
+
+- name: bamtools convert test_bamtools_convert_pileup
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_pileup -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.pileup
+      md5sum: e5a3cb4a3e1bf980a575fafce6a2826f
+    - path: output/bamtools/versions.yml
+      md5sum: fd3ad0edd1e085b1a002e0593d1d5814
+
+- name: bamtools convert test_bamtools_convert_sam
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_sam -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.sam
+      md5sum: 61ab3d0de16a9da8b651f9c692e19d5e
+    - path: output/bamtools/versions.yml
+      md5sum: 4be470ce3cc0143ae5ae415b612a4965
+
+- name: bamtools convert test_bamtools_convert_yaml
+  command: nextflow run tests/modules/bamtools/convert -entry test_bamtools_convert_yaml -c tests/config/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/convert
+  files:
+    - path: output/bamtools/test.yaml
+      md5sum: 68b56f198da036fef33e150eb773dc3b
+    - path: output/bamtools/versions.yml
+      md5sum: 1116abc088c5edf11bee393961c18b3e

tests/modules/freebayes/test.yml

@@ -1,34 +1,49 @@
 - name: freebayes test_freebayes
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 81d3e6ce7b6343d088b779567c3803eb
+    - path: output/freebayes/versions.yml
+      md5sum: 53651eb835af65df829241257584a7d2
 
 - name: freebayes test_freebayes_bed
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_bed -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 02645d014a63485162a7789007373b2a
+    - path: output/freebayes/versions.yml
+      md5sum: becc93c8a0be580c09d55b955d60a5e1
 
 - name: freebayes test_freebayes_cram
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_cram -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 3d0bfcd2129c62f8863952fa4c1054db
+    - path: output/freebayes/versions.yml
+      md5sum: 2e5b266edfc6cab81353cfc72c00f67c
 
 - name: freebayes test_freebayes_somatic
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 22fec868210ba3baf685b214bfd8e74b
+    - path: output/freebayes/versions.yml
+      md5sum: 8fbdb4c052fb3e42b5508a966125fa05
 
 - name: freebayes test_freebayes_somatic_cram_intervals
-  command: nextflow run ./tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c ./tests/config/nextflow.config -c ./tests/modules/freebayes/nextflow.config
+  command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
   tags:
     - freebayes
   files:
     - path: output/freebayes/test.vcf.gz
+      md5sum: 527cf2937067bbd4117d95fd472bb928
+    - path: output/freebayes/versions.yml
+      md5sum: af97e3dfdc086188739907c3460e49e0

tests/modules/gatk4/mergebamalignment/main.nf

@@ -6,11 +6,11 @@ include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalig
 
 workflow test_gatk4_mergebamalignment {
     input    = [ [ id:'test' ], // meta map
-                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
                ]
-    unmapped = file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
     fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
 
-    GATK4_MERGEBAMALIGNMENT ( input, unmapped, fasta, dict )
+    GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }

tests/modules/nextclade/datasetget/main.nf

@@ -8,7 +8,8 @@ workflow test_nextclade_datasetget {
 
     dataset = 'sars-cov-2'
     reference = 'MN908947'
-    tag = '2022-01-05T19:54:31Z'
+    tag = '2022-01-18T12:00:00Z'
 
     NEXTCLADE_DATASETGET ( dataset, reference, tag )
+
 }

tests/modules/nextclade/datasetget/test.yml

@@ -9,12 +9,14 @@
     - path: output/nextclade/sars-cov-2/primers.csv
       md5sum: 5990c3483bf66ce607aeb90a44e7ef2e
     - path: output/nextclade/sars-cov-2/qc.json
-      md5sum: 018fa0c0b0d2e824954e37e01495d549
+      md5sum: c512f51fda0212b21ffff05779180963
     - path: output/nextclade/sars-cov-2/reference.fasta
       md5sum: c7ce05f28e4ec0322c96f24e064ef55c
     - path: output/nextclade/sars-cov-2/sequences.fasta
       md5sum: 41129d255b99e0e92bdf20e866b99a1b
     - path: output/nextclade/sars-cov-2/tag.json
-      md5sum: 2f6d8e806d9064571ee4188ef1304c9c
+      md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3
     - path: output/nextclade/sars-cov-2/tree.json
-      md5sum: f8fb33ed62b59142ac20998eb599df6c
+      md5sum: b8f32f547ff9e2131d6fc66b68fc54b1
+    - path: output/nextclade/sars-cov-2/virus_properties.json
+      md5sum: 5f2de3949e07cb633f3d9e4a7654dc81

tests/modules/nextclade/run/main.nf

@@ -9,7 +9,7 @@ workflow test_nextclade_run {
 
     dataset = 'sars-cov-2'
     reference = 'MN908947'
-    tag = '2022-01-05T19:54:31Z'
+    tag = '2022-01-18T12:00:00Z'
 
     NEXTCLADE_DATASETGET ( dataset, reference, tag )
 
@@ -20,3 +20,4 @@ workflow test_nextclade_run {
 
     NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset )
 }
+

tests/modules/nextclade/run/test.yml

@@ -6,8 +6,8 @@
   files:
     - path: output/nextclade/test.json
     - path: output/nextclade/test.csv
-      md5sum: 3b87a4da190ba2e1fdc8418dc3a7ffdb
+      md5sum: 570c1aa2d5fd25c23d0042c1b06108e1
     - path: output/nextclade/test.tsv
-      md5sum: 449393288e8734a02def139c550a8d9b
+      md5sum: dd76e1a4c760785489be4e4a860b4d00
     - path: output/nextclade/test.tree.json
-      md5sum: 9c6e33cb7ff860bee6194847bd2c855c
+      md5sum: 3591b4dc1542995a7ffcffcb1f52b524

tests/test_versions_yml.py

@@ -16,7 +16,10 @@ def _get_workflow_names():
         # test_config = yaml.safe_load(f.read_text())
         test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
         for workflow in test_config:
-            yield workflow["name"]
+            # https://github.com/nf-core/modules/pull/1242 - added to cover tests 
+            # that expect an error and therefore will not generate a versions.yml
+            if 'exit_code' not in workflow: 
+                yield workflow["name"]
 
 
 @pytest.mark.workflow(*_get_workflow_names())