Merge branch 'nf-core:master' into master

modules/adapterremoval/main.nf

@@ -11,9 +11,15 @@ process ADAPTERREMOVAL {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path('*.fastq.gz'), emit: reads
-    tuple val(meta), path('*.log')     , emit: log
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path('*.truncated.gz')         , optional: true, emit: singles_truncated
+    tuple val(meta), path('*.discarded.gz')         , optional: true, emit: discarded
+    tuple val(meta), path('*.pair1.truncated.gz')   , optional: true, emit: pair1_truncated
+    tuple val(meta), path('*.pair2.truncated.gz')   , optional: true, emit: pair2_truncated
+    tuple val(meta), path('*.collapsed.gz')         , optional: true, emit: collapsed
+    tuple val(meta), path('*.collapsed.truncated')  , optional: true, emit: collapsed_truncated
+    tuple val(meta), path('*paired.gz')             , optional: true, emit: paired_interleaved
+    tuple val(meta), path('*.log')                  , emit: log
+    path "versions.yml"                             , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,30 +34,27 @@ process ADAPTERREMOVAL {
             --file1 $reads \\
             $args \\
             --basename $prefix \\
-            --threads $task.cpus \\
+            --threads ${task.cpus} \\
             --settings ${prefix}.log \\
-            --output1 ${prefix}.trimmed.fastq.gz \\
             --seed 42 \\
-            --gzip \\
+            --gzip
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
         END_VERSIONS
         """
-    } else if (!meta.single_end && !meta.collapse) {
+    } else if (!meta.single_end ) {
         """
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
             $args \\
             --basename $prefix \\
-            --threads $task.cpus \\
+            --threads ${task.cpus} \\
             --settings ${prefix}.log \\
-            --output1 ${prefix}.pair1.trimmed.fastq.gz \\
-            --output2 ${prefix}.pair2.trimmed.fastq.gz \\
             --seed 42 \\
-            --gzip \\
+            --gzip
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -63,13 +66,12 @@ process ADAPTERREMOVAL {
         AdapterRemoval  \\
             --file1 ${reads[0]} \\
             --file2 ${reads[1]} \\
-            --collapse \\
             $args \\
             --basename $prefix \\
             --threads $task.cpus \\
             --settings ${prefix}.log \\
             --seed 42 \\
-            --gzip \\
+            --gzip
 
         cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
         cat <<-END_VERSIONS > versions.yml

modules/adapterremoval/meta.yml

@@ -17,13 +17,13 @@ input:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false, collapse:false ]
+        e.g. [ id:'test', single_end:false ]
   - reads:
       type: file
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
-      pattern: "*.{fq,fastq,fg.gz,fastq.gz}"
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
 
 output:
   - meta:
@@ -31,12 +31,45 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  - reads:
+  - singles_truncated:
       type: file
       description: |
-        List of input adapter trimmed FastQ files of size 1 or 2 for
-        single-end or collapsed data and paired-end data, respectively.
-      pattern: "*.{fastq.gz}"
+        Adapter trimmed FastQ files of either single-end reads, or singleton
+        'orphaned' reads from merging of paired-end data (i.e., one of the pair
+        was lost due to filtering thresholds).
+      pattern: "*.truncated.gz"
+  - discarded:
+      type: file
+      description: |
+        Adapter trimmed FastQ files of reads that did not pass filtering
+        thresholds.
+      pattern: "*.discarded.gz"
+  - pair1_truncated:
+      type: file
+      description: |
+        Adapter trimmed R1 FastQ files of paired-end reads that did not merge
+        with their respective R2 pair due to long templates. The respective pair
+        is stored in 'pair2_truncated'.
+      pattern: "*.pair1.truncated.gz"
+  - pair2_truncated:
+      type: file
+      description: |
+        Adapter trimmed R2 FastQ files of paired-end reads that did not merge
+        with their respective R1 pair due to long templates. The respective pair
+        is stored in 'pair1_truncated'.
+      pattern: "*.pair2.truncated.gz"
+  - collapsed:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair but were not trimmed.
+      pattern: "*.collapsed.gz"
+  - collapsed_truncated:
+      type: file
+      description: |
+        Collapsed FastQ of paired-end reads that successfully merged with their
+        respective R1 pair and were trimmed of adapter due to sufficient overlap.
+      pattern: "*.collapsed.truncated.gz"
   - log:
       type: file
       description: AdapterRemoval log file
@@ -48,3 +81,4 @@ output:
 
 authors:
   - "@maxibor"
+  - "@jfy133"

modules/deepvariant/main.nf

@@ -17,8 +17,8 @@ process DEEPVARIANT {
     path(fai)
 
     output:
-    tuple val(meta), path("*.vcf.gz") ,  emit: vcf
-    tuple val(meta), path("*g.vcf.gz"),  emit: gvcf
+    tuple val(meta), path("${prefix}.vcf.gz") ,  emit: vcf
+    tuple val(meta), path("${prefix}.g.vcf.gz"),  emit: gvcf
     path "versions.yml"               ,  emit: versions
 
     when:
@@ -26,7 +26,7 @@ process DEEPVARIANT {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     def regions = intervals ? "--regions ${intervals}" : ""
 
     """

modules/faqcs/main.nf

@@ -13,6 +13,7 @@ process FAQCS {
     output:
     tuple val(meta), path('*.trimmed.fastq.gz')           , emit: reads
     tuple val(meta), path('*.stats.txt')                  , emit: stats
+    tuple val(meta), path('*.txt')                        , optional:true, emit: txt
     tuple val(meta), path('*_qc_report.pdf')              , optional:true, emit: statspdf
     tuple val(meta), path('*.log')                        , emit: log
     tuple val(meta), path('*.discard.fastq.gz')           , optional:true, emit: reads_fail

modules/faqcs/meta.yml

@@ -54,6 +54,10 @@ output:
       type: file
       description: trimming/qc text stats file
       pattern: "*.stats.txt"
+  - txt:
+      type: file
+      description: trimming/qc text txt files from --debug option
+      pattern: "*.txt"
   - statspdf:
       type: file
       description: trimming/qc pdf report file

modules/hamronization/deeparg/main.nf

@@ -0,0 +1,44 @@
+process HAMRONIZATION_DEEPARG {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
+        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+
+    input:
+    tuple val(meta), path(report)
+    val(format)
+    val(software_version)
+    val(reference_db_version)
+
+    output:
+    tuple val(meta), path("*.json"), optional: true, emit: json
+    tuple val(meta), path("*.tsv") , optional: true, emit: tsv
+    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}"
+    """
+    hamronize \\
+        deeparg \\
+        ${report} \\
+        $args \\
+        --format ${format} \\
+        --analysis_software_version ${software_version} \\
+        --reference_database_version ${reference_db_version} \\
+        --input_file_name ${prefix} \\
+        > ${prefix}.${format}
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+}

modules/hamronization/deeparg/meta.yml

@@ -0,0 +1,60 @@
+name: hamronization_deeparg
+description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
+keywords:
+  - amr
+  - antimicrobial resistance
+  - reporting
+  - deeparg
+tools:
+  - hamronization:
+      description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
+      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      tool_dev_url: https://github.com/pha4ge/hAMRonization
+      doi: ""
+      licence: ['GNU Lesser General Public v3 (LGPL v3)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - report:
+      type: file
+      description: Output .mapping.ARG file from DeepARG
+      pattern: "*.mapping.ARG"
+  - format:
+      type: value
+      description: Type of report file to be produced
+      pattern: "tsv|json"
+  - software_version:
+      type: value
+      description: Version of DeepARG used
+      pattern: "[0-9].[0-9].[0-9]"
+  - reference_db_version:
+      type: value
+      description: Database version of DeepARG used
+      pattern: "[0-9]"
+
+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"
+  - json:
+      type: file
+      description: hAMRonised report in JSON format
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: hAMRonised report in TSV format
+      pattern: "*.json"
+
+authors:
+  - "@jfy133"

modules/hamronization/summarize/main.nf

@@ -0,0 +1,38 @@
+process HAMRONIZATION_SUMMARIZE {
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/hamronization:1.0.3--py_0':
+        'quay.io/biocontainers/hamronization:1.0.3--py_0' }"
+
+    input:
+    path(reports)
+    val(format)
+
+    output:
+    path("hamronization_combined_report.json"), optional: true, emit: json
+    path("hamronization_combined_report.tsv") , optional: true, emit: tsv
+    path("hamronization_combined_report.html"), optional: true, emit: html
+    path "versions.yml"                       , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def outformat = format == 'interactive' ? 'html' : format
+    """
+    hamronize \\
+        summarize \\
+        ${reports.join(' ')} \\
+        -t ${format} \\
+        $args \\
+        -o hamronization_combined_report.${outformat}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+}

modules/hamronization/summarize/meta.yml

@@ -0,0 +1,45 @@
+name: hamronization_summarize
+description: Tool to summarize and combine all hAMRonization reports into a single file
+keywords:
+  - amr
+  - antimicrobial resistance
+  - reporting
+tools:
+  - hamronization:
+      description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
+      homepage: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
+      tool_dev_url: https://github.com/pha4ge/hAMRonization
+      doi: ""
+      licence: ['GNU Lesser General Public v3 (LGPL v3)']
+
+input:
+  - reports:
+      type: file
+      description: List of multiple hAMRonization reports in either JSON or TSV format
+      pattern: "*.{json,tsv}"
+  - format:
+      type: value
+      description: Type of final combined report file to be produced
+      pattern: "tsv|json|interactive"
+
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: hAMRonised summary in JSON format
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: hAMRonised summary in TSV format
+      pattern: "*.json"
+  - html:
+      type: file
+      description: hAMRonised summary in HTML format
+      pattern: "*.html"
+
+authors:
+  - "@jfy133"

modules/plink2/extract/main.nf

@@ -23,11 +23,13 @@ process PLINK2_EXTRACT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if( "$pgen" == "${prefix}.pgen" ) error "Input and output names are the same, use \"task.ext.prefix\" in modules.config to disambiguate!"
+    def mem_mb = task.memory.toMega()
     """
     plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
         --pfile ${pgen.baseName} \\
         $args \\
-        --threads $task.cpus \\
         --extract $variants \\
         --make-pgen vzs \\
         --out ${prefix}

modules/plink2/vcf/main.nf

@@ -11,10 +11,10 @@ process PLINK2_VCF {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*.pgen"), emit: pgen
-    tuple val(meta), path("*.psam"), emit: psam
-    tuple val(meta), path("*.pvar"), emit: pvar
-    path "versions.yml"            , emit: versions
+    tuple val(meta), path("*.pgen")    , emit: pgen
+    tuple val(meta), path("*.psam")    , emit: psam
+    tuple val(meta), path("*.pvar.zst"), emit: pvar
+    path "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,10 +22,14 @@ process PLINK2_VCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def mem_mb = task.memory.toMega()
     """
     plink2 \\
+        --threads $task.cpus \\
+        --memory $mem_mb \\
         $args \\
         --vcf $vcf \\
+        --make-pgen vzs \\
         --out ${prefix}
 
     cat <<-END_VERSIONS > versions.yml

modules/plink2/vcf/meta.yml

@@ -46,7 +46,7 @@ output:
   - pvar:
       type: file
       description: PLINK 2 variant information file
-      pattern: "*.{psam}"
+      pattern: "*.{pvar.zst}"
 
 authors:
   - "@nebfield"

modules/stranger/main.nf

@@ -0,0 +1,33 @@
+process STRANGER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
+        'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    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}"
+    """
+    stranger \\
+        $args \\
+        $vcf | gzip --no-name > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stranger: \$( stranger --version )
+    END_VERSIONS
+    """
+}

modules/stranger/meta.yml

@@ -0,0 +1,44 @@
+name: stranger
+description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
+keywords:
+  - STR
+  - repeat_expansions
+  - annotate
+  - vcf
+tools:
+  - stranger:
+      description: Annotate VCF files with str variants
+      homepage: https://github.com/moonso/stranger
+      documentation: https://github.com/moonso/stranger
+      tool_dev_url: https://github.com/moonso/stranger
+      doi: "10.5281/zenodo.4548873"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF with repeat expansions
+      pattern: "*.{vcf.gz,vcf}"
+
+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"
+  - vcf:
+      type: file
+      description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@ljmesi"

modules/untar/main.nf

@@ -2,7 +2,7 @@ process UNTAR {
     tag "$archive"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
+    conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
         'biocontainers/biocontainers:v1.2.0_cv1' }"

tests/config/pytest_modules.yml

@@ -752,6 +752,14 @@ gunzip:
   - modules/gunzip/**
   - tests/modules/gunzip/**
 
+hamronization/deeparg:
+  - modules/hamronization/deeparg/**
+  - tests/modules/hamronization/deeparg/**
+
+hamronization/summarize:
+  - modules/hamronization/summarize/**
+  - tests/modules/hamronization/summarize/**
+
 hicap:
   - modules/hicap/**
   - tests/modules/hicap/**
@@ -1565,6 +1573,10 @@ star/genomegenerate:
   - modules/star/genomegenerate/**
   - tests/modules/star/genomegenerate/**
 
+stranger:
+  - modules/stranger/**
+  - tests/modules/stranger/**
+
 strelka/germline:
   - modules/strelka/germline/**
   - tests/modules/strelka/germline/**

tests/config/test_data.config

@@ -68,7 +68,7 @@ params {
                 test_computematrix_mat_gz                      = "${test_data_dir}/genomics/sarscov2/illumina/deeptools/test.computeMatrix.mat.gz"
 
                 test_bcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.bcf"
-                
+
                 test_vcf                                       = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf"
                 test_vcf_gz                                    = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz"
                 test_vcf_gz_tbi                                = "${test_data_dir}/genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi"
@@ -321,6 +321,8 @@ params {
             'genome' {
                 genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
                 genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
+                genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
+
             }
             'illumina' {
                 test1_contigs_fa_gz             = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/illumina/fasta/test1.contigs.fa.gz"

tests/modules/adapterremoval/test.yml

@@ -1,31 +1,44 @@
 - name: adapterremoval test_adapterremoval_single_end
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_single_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_single_end -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
       md5sum: 2fd3d5d703b63ba33a83021fccf25f77
-    - path: output/adapterremoval/test.trimmed.fastq.gz
+    - path: output/adapterremoval/test.truncated.gz
       md5sum: 62139afee94defad5b83bdd0b8475a1f
+    - path: output/adapterremoval/versions.yml
+      md5sum: ac5b46719719b7ee62739530b80869fc
 
 - name: adapterremoval test_adapterremoval_paired_end
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
       md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
-    - path: output/adapterremoval/test.pair1.trimmed.fastq.gz
+    - path: output/adapterremoval/test.pair1.truncated.gz
       md5sum: 294a6277f0139bd597e57c6fa31f39c7
-    - path: output/adapterremoval/test.pair2.trimmed.fastq.gz
+    - path: output/adapterremoval/test.pair2.truncated.gz
       md5sum: de7b38e2c881bced8671acb1ab452d78
+    - path: output/adapterremoval/test.singleton.truncated.gz
+    - path: output/adapterremoval/versions.yml
+      md5sum: fa621c887897da5a379c719399c17db7
 
 - name: adapterremoval test_adapterremoval_paired_end_collapse
-  command: nextflow run ./tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c ./tests/config/nextflow.config -c ./tests/modules/adapterremoval/nextflow.config
+  command: nextflow run tests/modules/adapterremoval -entry test_adapterremoval_paired_end_collapse -c tests/config/nextflow.config
   tags:
     - adapterremoval
   files:
+    - path: output/adapterremoval/test.discarded.gz
     - path: output/adapterremoval/test.log
-      md5sum: 7f0b2328152226e46101a535cce718b3
-    - path: output/adapterremoval/test.merged.fastq.gz
-      md5sum: 07a8f725bfd3ecbeabdc41b32d898dee
+      md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
+    - path: output/adapterremoval/test.pair1.truncated.gz
+      md5sum: 294a6277f0139bd597e57c6fa31f39c7
+    - path: output/adapterremoval/test.pair2.truncated.gz
+      md5sum: de7b38e2c881bced8671acb1ab452d78
+    - path: output/adapterremoval/test.singleton.truncated.gz
+    - path: output/adapterremoval/versions.yml
+      md5sum: fd428f92a8446e0b34c5ae1c447215b8

tests/modules/faqcs/nextflow.config

@@ -1,5 +1,6 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    ext.args   = {"--debug" }
 
 }

tests/modules/faqcs/test.yml

@@ -3,8 +3,20 @@
   tags:
     - faqcs
   files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
+    - path: output/faqcs/test.base_content.txt
+      md5sum: f992603f01ca430c03c8aae02eba2f5d
     - path: output/faqcs/test.fastp.log
       md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: a3d462ab84151e982f99f85f52c21de3
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 80915f09fbaf5884c32e95acab2d031c
     - path: output/faqcs/test.stats.txt
       md5sum: ea20e93706b2e4c676004253baa3cec6
     - path: output/faqcs/test.trimmed.fastq.gz
@@ -18,8 +30,20 @@
   tags:
     - faqcs
   files:
+    - path: output/faqcs/qa.test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
+    - path: output/faqcs/qa.test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/qa.test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
+    - path: output/faqcs/test.base_content.txt
+      md5sum: 99aa9a775ccd8d6503f0cf80f775203c
     - path: output/faqcs/test.fastp.log
       md5sum: be79dc893f87de1f82faf749cdfb848c
+    - path: output/faqcs/test.for_qual_histogram.txt
+      md5sum: 4f4b131be5425bdfa4b3237e44fa7d48
+    - path: output/faqcs/test.length_count.txt
+      md5sum: 420298983c762754d5b0ef32c9d5dad4
     - path: output/faqcs/test.stats.txt
       md5sum: 9a693f8af94ab8c485519d9a523aa622
     - path: output/faqcs/test_1.trimmed.fastq.gz

tests/modules/hamronization/deeparg/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG } from '../../../../modules/hamronization/deeparg/main.nf'
+
+workflow test_hamronization_deeparg {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+}

tests/modules/hamronization/deeparg/nextflow.config

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

tests/modules/hamronization/deeparg/test.yml

@@ -0,0 +1,8 @@
+- name: hamronization deeparg test_hamronization_deeparg
+  command: nextflow run tests/modules/hamronization/deeparg -entry test_hamronization_deeparg -c tests/config/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/deeparg
+  files:
+    - path: output/hamronization/test.tsv
+      md5sum: 3c315605aca0c5964796bb5fd4cdd522

tests/modules/hamronization/summarize/main.nf

@@ -0,0 +1,36 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HAMRONIZATION_DEEPARG                                 } from '../../../../modules/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_DEEPARG as HAMRONIZATION_DEEPARG_SECOND } from '../../../../modules/hamronization/deeparg/main.nf'
+include { HAMRONIZATION_SUMMARIZE                               } from '../../../../modules/hamronization/summarize/main.nf'
+
+workflow test_hamronization_summarize {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    input2 = [
+        [ id:'test2', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
+    ]
+
+    HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2'  )
+    HAMRONIZATION_DEEPARG_SECOND ( input2, 'tsv', '1.0.2', '2' )
+
+    ch_deeparg_run_one = HAMRONIZATION_DEEPARG.out.tsv
+    ch_deeparg_run_two = HAMRONIZATION_DEEPARG_SECOND.out.tsv
+
+    ch_deeparg_run_one
+        .mix( ch_deeparg_run_two )
+        .map{
+            [ it[1] ]
+        }
+        .collect()
+        .set { ch_input_for_summarize }
+
+    HAMRONIZATION_SUMMARIZE ( ch_input_for_summarize , 'json' )
+}

tests/modules/hamronization/summarize/nextflow.config

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

tests/modules/hamronization/summarize/test.yml

@@ -0,0 +1,14 @@
+- name: hamronization summarize test_hamronization_summarize
+  command: nextflow run tests/modules/hamronization/summarize -entry test_hamronization_summarize -c tests/config/nextflow.config
+  tags:
+    - hamronization
+    - hamronization/summarize
+  files:
+    - path: output/hamronization/hamronization_combined_report.json
+      md5sum: 1623b6cc3b213208a425e023edd94691
+    - path: output/hamronization/test.tsv
+      md5sum: 3c315605aca0c5964796bb5fd4cdd522
+    - path: output/hamronization/test2.tsv
+      md5sum: 453f38502e35261a50a0849dca34f05b
+    - path: output/hamronization/versions.yml
+      md5sum: 99b5046fac643e16ca3362d1baf3284b

tests/modules/plink2/vcf/test.yml

@@ -1,12 +1,14 @@
 - name: plink2 vcf test_plink2_vcf
-  command: nextflow run ./tests/modules/plink2/vcf -entry test_plink2_vcf -c ./tests/config/nextflow.config -c ./tests/modules/plink2/vcf/nextflow.config
+  command: nextflow run tests/modules/plink2/vcf -entry test_plink2_vcf -c tests/config/nextflow.config
   tags:
-    - plink2/vcf
     - plink2
+    - plink2/vcf
   files:
     - path: output/plink2/test.pgen
       md5sum: d66d3cd4a6c9cca1a4073d7f4b277041
     - path: output/plink2/test.psam
       md5sum: dc3b77d7753a7bed41734323e3549b10
-    - path: output/plink2/test.pvar
-      md5sum: d61e53f847a6335138b584216b4e45d0
+    - path: output/plink2/test.pvar.zst
+      md5sum: b53cccb83e024a39789af5eab8de1c28
+    - path: output/plink2/versions.yml
+      md5sum: 82ada74bc81473b7cba377f696acf54c

tests/modules/stranger/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
+include { STRANGER } from '../../../modules/stranger/main.nf'
+
+workflow test_stranger {
+
+    input = [ [ id:'test', gender:'male' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
+
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf )
+}

tests/modules/stranger/nextflow.config

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

tests/modules/stranger/test.yml

@@ -0,0 +1,13 @@
+- name: stranger test_stranger
+  command: nextflow run tests/modules/stranger -entry test_stranger -c tests/config/nextflow.config
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
+    - path: output/expansionhunter/versions.yml
+      md5sum: f3962a6eecfddf9682414c0f605a885a
+    - path: output/stranger/test.vcf.gz
+      md5sum: bbe15159195681d5c18596d3ad85c78f
+    - path: output/stranger/versions.yml
+      md5sum: 5ec35fd835fb1be50bc3e7c004310fc0