Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,64 +0,0 @@
----
-name: Bug report
-about: Report something that is broken or incorrect
-title: "[BUG]"
----
-
-<!--
-# nf-core/module bug report
-
-Hi there!
-
-Thanks for telling us about a problem with the modules.
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Check Documentation
-
-I have checked the following places for your error:
-
-- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/module documentation](https://github.com/nf-core/modules/blob/master/README.md)
-
-## Description of the bug
-
-<!-- A clear and concise description of what the bug is. -->
-
-## Steps to reproduce
-
-Steps to reproduce the behaviour:
-
-1. Command line: <!-- [e.g. `nextflow run ...`] -->
-2. See error: <!-- [Please provide your error message] -->
-
-## Expected behaviour
-
-<!-- A clear and concise description of what you expected to happen. -->
-
-## Log files
-
-Have you provided the following extra information/files:
-
-- [ ] The command used to run the module
-- [ ] The `.nextflow.log` file <!-- this is a hidden file in the directory where you launched the module -->
-
-## System
-
-- Hardware: <!-- [e.g. HPC, Desktop, Cloud...] -->
-- Executor: <!-- [e.g. slurm, local, awsbatch...] -->
-- OS: <!-- [e.g. CentOS Linux, macOS, Linux Mint...] -->
-- Version <!-- [e.g. 7, 10.13.6, 18.3...] -->
-
-## Nextflow Installation
-
-- Version: <!-- [e.g. 19.10.0] -->
-
-## Container engine
-
-- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
-- version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/module:2.6] -->
-
-## Additional context
-
-<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,52 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: checkboxes
+    attributes:
+      label: Have you checked the docs?
+      description: I have checked the following places for my error
+      options:
+        - label: "[nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)"
+          required: true
+        - label: "[nf-core modules documentation](https://nf-co.re/docs/contributing/modules)"
+          required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine and version: _(e.g. Docker 1.0.0, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS and version: _(eg. CentOS Linux, macOS, Ubuntu 22.04)_
+        * Image tag: <!-- [e.g. nfcore/cellranger:2.6] -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,32 +0,0 @@
----
-name: Feature request
-about: Suggest an idea for nf-core/modules
-title: "[FEATURE]"
----
-
-<!--
-# nf-core/modules feature request
-
-Hi there!
-
-Thanks for suggesting a new feature for the modules!
-Please delete this text and anything that's not relevant from the template below:
--->
-
-## Is your feature request related to a problem? Please describe
-
-<!-- A clear and concise description of what the problem is. -->
-
-<!-- e.g. [I'm always frustrated when ...] -->
-
-## Describe the solution you'd like
-
-<!-- A clear and concise description of what you want to happen. -->
-
-## Describe alternatives you've considered
-
-<!-- A clear and concise description of any alternative solutions or features you've considered. -->
-
-## Additional context
-
-<!-- Add any other context about the feature request here. -->

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,32 @@
+name: Feature request
+description: Suggest an idea for nf-core/modules
+labels: feature
+title: "[FEATURE]"
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Is your feature request related to a problem? Please describe
+      description: A clear and concise description of what the bug is.
+      placeholder: |
+        <!-- e.g. [I'm always frustrated when ...] -->
+    validations:
+      required: true
+
+  - type: textarea
+    id: solution
+    attributes:
+      label: Describe the solution you'd like
+      description: A clear and concise description of the solution you want to happen.
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Describe alternatives you've considered
+      description: A clear and concise description of any alternative solutions or features you've considered.
+
+  - type: textarea
+    id: additional_context
+    attributes:
+      label: Additional context
+      description: Add any other context about the feature request here.

.github/ISSUE_TEMPLATE/new_module.md

@@ -1,26 +0,0 @@
----
-name: New module
-about: Suggest a new module for nf-core/modules
-title: "new module: TOOL/SUBTOOL"
-label: new module
----
-
-<!--
-# nf-core/modules new module suggestion
-
-Hi there!
-
-Thanks for suggesting a new module for the modules!
-Please delete this text and anything that's not relevant from the template below:
-
-Replace TOOL with the bioconda name for the tool in the following text, so that the link is functional.
-
-Replace TOOL/SUBTOOL in the issue title so that it's understandable.
--->
-
-I think it would be good to have a module for [TOOL](https://bioconda.github.io/recipes/TOOL/README.html)
-
-- [ ] This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
-- [ ] There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
-- [ ] There is no [open issue](https://github.com/nf-core/modules/issues) for this module
-- [ ] If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module

.github/ISSUE_TEMPLATE/new_module.yml

@@ -0,0 +1,36 @@
+name: New module
+description: Suggest a new module for nf-core/modules
+title: "new module: TOOL/SUBTOOL"
+labels: new module
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing module for this?
+      description: This module does not exist yet with the [`nf-core modules list`](https://github.com/nf-core/tools#list-modules) command
+      options:
+        - label: I have searched for the existing module
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open PR for this?
+      description: There is no [open pull request](https://github.com/nf-core/modules/pulls) for this module
+      options:
+        - label: I have searched for existing PRs
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Is there an open issue for this?
+      description: There is no [open issue](https://github.com/nf-core/modules/issues) for this module
+      options:
+        - label: I have searched for existing issues
+          required: true
+
+  - type: checkboxes
+    attributes:
+      label: Are you going to work on this?
+      description: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+      options:
+        - label: If I'm planning to work on this module, I added myself to the `Assignees` to facilitate tracking who is working on the module
+          required: false

modules/antismash/antismashlitedownloaddatabases/main.nf

@@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
 
     /*
-    These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input 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. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
+    These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input 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. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
     Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
+    These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
     */
 
     containerOptions {
@@ -26,6 +27,9 @@ 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 "versions.yml", emit: versions
 
     when:
@@ -40,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        antismash: \$(antismash --version | sed 's/antiSMASH //')
+        antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
     END_VERSIONS
     """
 }

modules/antismash/antismashlitedownloaddatabases/meta.yml

@@ -27,17 +27,17 @@ input:
   - database_css:
       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 use 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.
+        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"
   - database_detection:
       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 use 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.
+        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"
   - database_modules:
       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 use 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.
+        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"
 
 output:
@@ -50,6 +50,21 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
+  - css_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"
 
 authors:
   - "@jasmezz"

modules/bamtools/split/main.nf

@@ -2,10 +2,10 @@ process BAMTOOLS_SPLIT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
+    conda (params.enable_conda ? "bioconda::bamtools=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
+        'https://depot.galaxyproject.org/singularity/bamtools:2.5.2--hd03093a_0' :
-        'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
+        'quay.io/biocontainers/bamtools:2.5.2--hd03093a_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -20,10 +20,14 @@ process BAMTOOLS_SPLIT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_list = bam.collect{"-in $it"}.join(' ')
     """
     bamtools \\
+        merge \\
+        $input_list \\
+        | bamtools \\
             split \\
-        -in $bam \\
+            -stub $prefix \\
             $args
 
     cat <<-END_VERSIONS > versions.yml

modules/bamtools/split/meta.yml

@@ -23,7 +23,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - bam:
       type: file
-      description: A BAM file to split
+      description: A list of one or more BAM files to merge and then split
       pattern: "*.bam"
 
 output:
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sguizard"
+  - "@matthdsm"

modules/custom/getchromsizes/main.nf

@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     path fasta

modules/diamond/blastp/main.nf

@@ -2,19 +2,25 @@ process DIAMOND_BLASTP {
     tag "$meta.id"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     tuple val(meta), path(fasta)
     path db
+    val out_ext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"               , emit: versions
 
     when:
@@ -23,6 +29,21 @@ process DIAMOND_BLASTP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
+    switch ( out_ext ) {
+        case "blast": outfmt = 0; break
+        case "xml": outfmt = 5; break
+        case "txt": outfmt = 6; break
+        case "daa": outfmt = 100; break
+        case "sam": outfmt = 101; break
+        case "tsv": outfmt = 102; break
+        case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
+    }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
 
@@ -31,8 +52,9 @@ process DIAMOND_BLASTP {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.txt
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/diamond/blastp/meta.yml

@@ -28,12 +28,50 @@ input:
       type: directory
       description: Directory containing the protein blast database
       pattern: "*"
+  - out_ext:
+      type: string
+      description: |
+        Specify the type of output file to be generated. `blast` corresponds to
+        BLAST pairwise format. `xml` corresponds to BLAST xml format.
+        `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
+        taxonomic classification format.
+      pattern: "blast|xml|txt|daa|sam|tsv|paf"
+  - blast_columns:
+      type: string
+      description: |
+        Optional space separated list of DIAMOND tabular BLAST output keywords
+        used for in conjunction with the 'txt' out_ext option (--outfmt 6). See
+        DIAMOND documnetation for more information.
 
 output:
-  - txt:
+  - blast:
       type: file
       description: File containing blastp hits
-      pattern: "*.{blastp.txt}"
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
+  - txt:
+      type: file
+      description: File containing hits in tabular BLAST format.
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
@@ -41,3 +79,4 @@ output:
 
 authors:
   - "@spficklin"
+  - "@jfy133"

modules/diamond/blastx/main.nf

@@ -2,19 +2,25 @@ process DIAMOND_BLASTX {
     tag "$meta.id"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? "bioconda::diamond=2.0.9" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     tuple val(meta), path(fasta)
     path db
+    val out_ext
+    val blast_columns
 
     output:
-    tuple val(meta), path('*.txt'), emit: txt
+    tuple val(meta), path('*.blast'), optional: true, emit: blast
+    tuple val(meta), path('*.xml')  , optional: true, emit: xml
+    tuple val(meta), path('*.txt')  , optional: true, emit: txt
+    tuple val(meta), path('*.daa')  , optional: true, emit: daa
+    tuple val(meta), path('*.sam')  , optional: true, emit: sam
+    tuple val(meta), path('*.tsv')  , optional: true, emit: tsv
+    tuple val(meta), path('*.paf')  , optional: true, emit: paf
     path "versions.yml"                               , emit: versions
 
     when:
@@ -23,6 +29,21 @@ process DIAMOND_BLASTX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def columns = blast_columns ? "${blast_columns}" : ''
+    switch ( out_ext ) {
+        case "blast": outfmt = 0; break
+        case "xml": outfmt = 5; break
+        case "txt": outfmt = 6; break
+        case "daa": outfmt = 100; break
+        case "sam": outfmt = 101; break
+        case "tsv": outfmt = 102; break
+        case "paf": outfmt = 103; break
+        default:
+            outfmt = '6';
+            out_ext = 'txt';
+            log.warn("Unknown output file format provided (${out_ext}): selecting DIAMOND default of tabular BLAST output (txt)");
+            break
+    }
     """
     DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`
 
@@ -31,8 +52,9 @@ process DIAMOND_BLASTX {
         --threads $task.cpus \\
         --db \$DB \\
         --query $fasta \\
+        --outfmt ${outfmt} ${columns} \\
         $args \\
-        --out ${prefix}.txt
+        --out ${prefix}.${out_ext}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/diamond/blastx/meta.yml

@@ -28,12 +28,44 @@ input:
       type: directory
       description: Directory containing the nucelotide blast database
       pattern: "*"
+  - out_ext:
+      type: string
+      description: |
+        Specify the type of output file to be generated. `blast` corresponds to
+        BLAST pairwise format. `xml` corresponds to BLAST xml format.
+        `txt` corresponds to to BLAST tabular format. `tsv` corresponds to
+        taxonomic classification format.
+      pattern: "blast|xml|txt|daa|sam|tsv|paf"
 
 output:
+  - blast:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{blast}"
+  - xml:
+      type: file
+      description: File containing blastp hits
+      pattern: "*.{xml}"
   - txt:
       type: file
-      description: File containing blastx hits
+      description: File containing hits in tabular BLAST format.
-      pattern: "*.{blastx.txt}"
+      pattern: "*.{txt}"
+  - daa:
+      type: file
+      description: File containing hits DAA format
+      pattern: "*.{daa}"
+  - sam:
+      type: file
+      description: File containing aligned reads in SAM format
+      pattern: "*.{sam}"
+  - tsv:
+      type: file
+      description: Tab separated file containing taxonomic classification of hits
+      pattern: "*.{tsv}"
+  - paf:
+      type: file
+      description: File containing aligned reads in pairwise mapping format format
+      pattern: "*.{paf}"
   - versions:
       type: file
       description: File containing software versions
@@ -41,3 +73,4 @@ output:
 
 authors:
   - "@spficklin"
+  - "@jfy133"

modules/diamond/makedb/main.nf

@@ -2,12 +2,10 @@ process DIAMOND_MAKEDB {
     tag "$fasta"
     label 'process_medium'
 
-    // Dimaond is limited to v2.0.9 because there is not a
+    conda (params.enable_conda ? "bioconda::diamond=2.0.15" : null)
-    // singularity version higher than this at the current time.
-    conda (params.enable_conda ? 'bioconda::diamond=2.0.9' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/diamond:2.0.9--hdcc8f71_0' :
+        'https://depot.galaxyproject.org/singularity/diamond:2.0.15--hb97b32f_0' :
-        'quay.io/biocontainers/diamond:2.0.9--hdcc8f71_0' }"
+        'quay.io/biocontainers/diamond:2.0.15--hb97b32f_0' }"
 
     input:
     path fasta

modules/elprep/merge/main.nf

@@ -0,0 +1,43 @@
+process ELPREP_MERGE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
+        'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("output/**.{bam,sam}")    , emit: 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 suffix      = args.contains("--output-type sam") ? "sam" : "bam"
+    def single_end  = meta.single_end ? " --single-end" : ""
+
+    """
+    # create directory and move all input so elprep can find and merge them before splitting
+    mkdir input
+    mv ${bam} input/
+
+    elprep merge \\
+        input/ \\
+        output/${prefix}.${suffix} \\
+        $args \\
+        ${single_end} \\
+        --nr-of-threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
+    END_VERSIONS
+    """
+}

modules/elprep/merge/meta.yml

@@ -0,0 +1,44 @@
+name: "elprep_merge"
+description: Merge split bam/sam chunks in one file
+keywords:
+  - bam
+  - sam
+  - merge
+tools:
+  - "elprep":
+      description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
+      homepage: "https://github.com/ExaScience/elprep"
+      documentation: "https://github.com/ExaScience/elprep"
+      tool_dev_url: "https://github.com/ExaScience/elprep"
+      doi: "10.1371/journal.pone.0244471"
+      licence: "['AGPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: List of BAM/SAM chunks to merge
+      pattern: "*.{bam,sam}"
+
+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"
+  - bam:
+      type: file
+      description: Merged BAM/SAM file
+      pattern: "*.{bam,sam}"
+
+authors:
+  - "@matthdsm"

modules/gatk4/haplotypecaller/main.nf

@@ -17,7 +17,7 @@ process GATK4_HAPLOTYPECALLER {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    tuple val(meta), path("*.tbi")   , emit: tbi
+    tuple val(meta), path("*.tbi")   , optional:true, emit: tbi
     path "versions.yml"              , emit: versions
 
     when:

modules/gatk4/markduplicates/main.nf

@@ -12,7 +12,7 @@ process GATK4_MARKDUPLICATES {
 
     output:
     tuple val(meta), path("*.bam")    , emit: bam
-    tuple val(meta), path("*.bai")    , emit: bai
+    tuple val(meta), path("*.bai")    , optional:true, emit: bai
     tuple val(meta), path("*.metrics"), emit: metrics
     path "versions.yml"               , emit: versions
 

modules/gatk4/splitncigarreads/main.nf

@@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS {
         'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai), path(intervals)
     path  fasta
     path  fai
     path  dict
@@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def interval_command = intervals ? "--intervals $intervals" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS {
         --input $bam \\
         --output ${prefix}.bam \\
         --reference $fasta \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 

modules/gatk4/splitncigarreads/meta.yml

@@ -23,6 +23,13 @@ input:
       type: list
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
+  - bai:
+      type: list
+      description: BAI/SAI/CRAI index file (optional)
+      pattern: "*.{bai,sai,crai}"
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
   - fasta:
       type: file
       description: The reference fasta file

modules/krona/ktimporttext/main.nf

@@ -0,0 +1,34 @@
+process KRONA_KTIMPORTTEXT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
+        'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(report)
+
+    output:
+    tuple val(meta), path ('*.html'), emit: html
+    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}"
+    """
+    ktImportText  \\
+        $args \\
+        -o ${prefix}.html \\
+        $report
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
+    END_VERSIONS
+    """
+}

modules/krona/ktimporttext/meta.yml

@@ -0,0 +1,47 @@
+name: "krona_ktimporttext"
+description: Creates a Krona chart from text files listing quantities and lineages.
+keywords:
+  - plot
+  - taxonomy
+  - interactive
+  - html
+  - visualisation
+  - krona chart
+  - metagenomics
+tools:
+  - krona:
+      description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
+      homepage: https://github.com/marbl/Krona/wiki/KronaTools
+      documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html
+      tool_dev_url: https://github.com/marbl/Krona
+      doi: 10.1186/1471-2105-12-385
+      licence: https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test']
+  - report:
+      type: file
+      description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored."
+      pattern: "*.{txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - html:
+      type: file
+      description: A html file containing an interactive krona plot.
+      pattern: "*.{html}"
+
+authors:
+  - "@jianhong"

modules/minimap2/align/main.nf

@@ -2,17 +2,21 @@ process MINIMAP2_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
-        'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+        'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
 
     input:
     tuple val(meta), path(reads)
     path reference
+    val bam_format
+    val cigar_paf_format
+    val cigar_bam
 
     output:
-    tuple val(meta), path("*.paf"), emit: paf
+    tuple val(meta), path("*.paf"), optional: true, emit: paf
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
     path "versions.yml"           , emit: versions
 
     when:
@@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
+    def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
+    def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\
         -t $task.cpus \\
         $reference \\
         $input_reads \\
-        > ${prefix}.paf
+        $cigar_paf \\
+        $set_cigar_bam \\
+        $bam_output
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/minimap2/align/meta.yml

@@ -29,6 +29,17 @@ input:
       type: file
       description: |
         Reference database in FASTA format.
+  - bam_format:
+      type: boolean
+      description: Specify that output should be in BAM format
+  - cigar_paf_format:
+      type: boolean
+      description: Specify that output CIGAR should be in PAF format
+  - cigar_bam:
+      type: boolean
+      description: |
+        Write CIGAR with >65535 ops at the CG tag. This is recommended when
+        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
   - meta:
       type: map
@@ -39,9 +50,16 @@ output:
       type: file
       description: Alignment in PAF format
       pattern: "*.paf"
+  - bam:
+      type: file
+      description: Alignment in BAM format
+      pattern: "*.bam"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@heuermh"
+  - "@sofstam"
+  - "@sateeshperi"
+  - "@jfy133"

modules/phantompeakqualtools/main.nf

@@ -23,10 +23,11 @@ process PHANTOMPEAKQUALTOOLS {
 
     script:
     def args   = task.ext.args ?: ''
+    def args2  = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     RUN_SPP=`which run_spp.R`
-    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out"
+    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/addorreplacereadgroups/main.nf

@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -38,12 +38,12 @@ process PICARD_ADDORREPLACEREADGROUPS {
         -Xmx${avail_mem}g \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
-        -ID ${ID} \\
+        --RGID ${ID} \\
-        -LB ${LIBRARY} \\
+        --RGLB ${LIBRARY} \\
-        -PL ${PLATFORM} \\
+        --RGPL ${PLATFORM} \\
-        -PU ${BARCODE} \\
+        --RGPU ${BARCODE} \\
-        -SM ${SAMPLE} \\
+        --RGSM ${SAMPLE} \\
-        -CREATE_INDEX true
+        --CREATE_INDEX true
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/cleansam/main.nf

@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${bam} \\
+        --INPUT ${bam} \\
-        -O ${prefix}.bam
+        --OUTPUT ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/collecthsmetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
         CollectHsMetrics \\
         $args \\
         $reference \\
-        -BAIT_INTERVALS $bait_intervals \\
+        --BAIT_INTERVALS $bait_intervals \\
-        -TARGET_INTERVALS $target_intervals \\
+        --TARGET_INTERVALS $target_intervals \\
-        -INPUT $bam \\
+        --INPUT $bam \\
-        -OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
+        --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
 
 
     cat <<-END_VERSIONS > versions.yml

modules/picard/collectmultiplemetrics/main.nf

@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         -Xmx${avail_mem}g \\
         CollectMultipleMetrics \\
         $args \\
-        INPUT=$bam \\
+        --INPUT $bam \\
-        OUTPUT=${prefix}.CollectMultipleMetrics \\
+        --OUTPUT ${prefix}.CollectMultipleMetrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/collectwgsmetrics/main.nf

@@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam)
     path  fasta
 
     output:
@@ -32,9 +32,10 @@ process PICARD_COLLECTWGSMETRICS {
         -Xmx${avail_mem}g \\
         CollectWgsMetrics \\
         $args \\
-        INPUT=$bam \\
+        --INPUT $bam \\
-        OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
+        --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --REFERENCE_SEQUENCE $fasta
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/createsequencedictionary/main.nf

@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        R=$fasta \\
+        --REFERENCE $fasta \\
-        O=${prefix}.dict
+        --OUTPUT ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/crosscheckfingerprints/main.nf

@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)

modules/picard/filtersamreads/main.nf

@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)

modules/picard/fixmateinformation/main.nf

@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
     picard \\
         FixMateInformation \\
         -Xmx${avail_mem}g \\
-        -I ${bam} \\
+        --INPUT ${bam} \\
-        -O ${prefix}.bam \\
+        --OUTPUT ${prefix}.bam \\
         --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml

modules/picard/liftovervcf/main.nf

@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
@@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
         -Xmx${avail_mem}g \\
         LiftoverVcf \\
         $args \\
-        I=$input_vcf \\
+        --INPUT $input_vcf \\
-        O=${prefix}.lifted.vcf.gz \\
+        --OUTPUT ${prefix}.lifted.vcf.gz \\
-        CHAIN=$chain \\
+        --CHAIN $chain \\
-        REJECT=${prefix}.unlifted.vcf.gz \\
+        --REJECT ${prefix}.unlifted.vcf.gz \\
-        R=$fasta
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/markduplicates/main.nf

@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $args \\
-        I=$bam \\
+        --INPUT $bam \\
-        O=${prefix}.bam \\
+        --OUTPUT ${prefix}.bam \\
-        M=${prefix}.MarkDuplicates.metrics.txt
+        --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/picard/mergesamfiles/main.nf

@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
@@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
             -Xmx${avail_mem}g \\
             MergeSamFiles \\
             $args \\
-            ${'INPUT='+bam_files.join(' INPUT=')} \\
+            ${'--INPUT '+bam_files.join(' --INPUT ')} \\
-            OUTPUT=${prefix}.bam
+            --OUTPUT ${prefix}.bam
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)

modules/picard/sortsam/main.nf

@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)

modules/picard/sortvcf/main.nf

@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -22,8 +22,8 @@ process PICARD_SORTVCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
+    def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
-    def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
+    def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'

modules/rsem/calculateexpression/main.nf

@@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     tuple val(meta), path(reads)

modules/rsem/preparereference/main.nf

@@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE {
     tag "$fasta"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     path fasta, stageAs: "rsem/*"

modules/samtools/bamtocram/main.nf

@@ -0,0 +1,35 @@
+//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
+process SAMTOOLS_BAMTOCRAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input), path(index)
+    path  fasta
+    path  fai
+
+    output:
+    tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
+    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}"
+    """
+    samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
+    samtools index -@${task.cpus} ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}

modules/samtools/bamtocram/meta.yml

@@ -0,0 +1,52 @@
+name: samtools_bamtocram
+description: filter/convert and then index CRAM file
+keywords:
+  - view
+  - index
+  - bam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+  - index:
+      type: file
+      description: BAM/SAM index file
+      pattern: "*.{bai,sai}"
+  - fasta:
+      type: file
+      description: Reference file to create the CRAM file
+      pattern: "*.{fasta,fa}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram_crai:
+      type: file
+      description: filtered/converted CRAM file + index
+      pattern: "*{.cram,.crai}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@FriederikeHanssen"
+  - "@maxulysse"

modules/tabix/tabix/main.nf

@@ -11,7 +11,8 @@ process TABIX_TABIX {
     tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("*.tbi"), emit: tbi
+    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
+    tuple val(meta), path("*.csi"), optional:true, emit: csi
     path  "versions.yml"          , emit: versions
 
     when:

modules/tabix/tabix/meta.yml

@@ -31,6 +31,10 @@ output:
       type: file
       description: tabix index file
       pattern: "*.{tbi}"
+  - csi:
+      type: file
+      description: coordinate sorted index file
+      pattern: "*.{csi}"
   - versions:
       type: file
       description: File containing software versions

modules/tiddit/sv/main.nf

@@ -24,7 +24,7 @@ process TIDDIT_SV {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta == "dummy_file.txt" ? "--ref $fasta" : ""
+    def reference = fasta ? "--ref $fasta" : ""
     """
     tiddit \\
         --sv \\

modules/trimgalore/main.nf

@@ -11,12 +11,13 @@ process TRIMGALORE {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fq.gz")    , emit: reads
+    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
-    tuple val(meta), path("*report.txt"), emit: log
+    tuple val(meta), path("*report.txt")          , emit: log
     path "versions.yml"                           , emit: versions
 
-    tuple val(meta), path("*.html"), emit: html optional true
+    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
-    tuple val(meta), path("*.zip") , emit: zip optional true
+    tuple val(meta), path("*.html")               , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,6 +53,7 @@ process TRIMGALORE {
             $c_r1 \\
             $tpc_r1 \\
             ${prefix}.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@@ -73,6 +75,7 @@ process TRIMGALORE {
             $tpc_r2 \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')

modules/trimgalore/meta.yml

@@ -37,6 +37,11 @@ output:
         List of input adapter trimmed FastQ files of size 1 and 2 for
         single-end and paired-end data, respectively.
       pattern: "*.{fq.gz}"
+  - unpaired:
+      type: file
+      description: |
+        FastQ files containing unpaired reads from read 1 or read 2
+      pattern: "*unpaired*.fq.gz"
   - html:
       type: file
       description: FastQC report (optional)

subworkflows/nf-core/bam_qc_picard/main.nf

@@ -0,0 +1,41 @@
+//
+// Run QC steps on BAM/CRAM files using Picard
+//
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picard/collectwgsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecthsmetrics/main'
+
+workflow BAM_QC_PICARD {
+    take:
+    ch_bam              // channel: [ val(meta), [ bam ]]
+    ch_fasta            // channel: [ fasta ]
+    ch_fasta_fai        // channel: [ fasta_fai ]
+    ch_bait_interval    // channel: [ bait_interval ]
+    ch_target_interval  // channel: [ target_interval ]
+
+    main:
+    ch_versions = Channel.empty()
+    ch_coverage_metrics = Channel.empty()
+
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+
+    if (ch_bait_interval || ch_target_interval) {
+        if (!ch_bait_interval) log.error("Bait interval channel is empty")
+        if (!ch_target_interval) log.error("Target interval channel is empty")
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+    } else {
+        PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
+        ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
+    }
+
+    emit:
+    coverage_metrics    = ch_coverage_metrics                       // channel: [ val(meta), [ coverage_metrics ] ]
+    multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
+
+    versions            = ch_versions                               // channel: [ versions.yml ]
+}

subworkflows/nf-core/bam_qc_picard/meta.yml

@@ -0,0 +1,60 @@
+name: bam_qc
+description: Produces comprehensive statistics from BAM file
+keywords:
+  - statistics
+  - counts
+  - hs_metrics
+  - wgs_metrics
+  - bam
+  - sam
+  - cram
+modules:
+  - picard/collectmultiplemetrics
+  - picard/collectwgsmetrics
+  - picard/collecthsmetrics
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - fasta:
+      type: optional file
+      description: Reference fasta file
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: optional file
+      description: Reference fasta file index
+      pattern: "*.{fasta,fa}.fai"
+  - bait_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the baits used.
+      pattern: "baits.interval_list"
+  - target_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the targets.
+      pattern: "targets.interval_list"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - coverage_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
+      pattern: "*_metrics.txt"
+  - multiple_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectMultipleMetrics
+      pattern: "*_{metrics}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"

tests/config/pytest_modules.yml

@@ -607,6 +607,10 @@ elprep/filter:
   - modules/elprep/filter/**
   - tests/modules/elprep/filter/**
 
+elprep/merge:
+  - modules/elprep/merge/**
+  - tests/modules/elprep/merge/**
+
 elprep/split:
   - modules/elprep/split/**
   - tests/modules/elprep/split/**
@@ -1054,6 +1058,10 @@ krona/ktimporttaxonomy:
   - modules/krona/ktimporttaxonomy/**
   - tests/modules/krona/ktimporttaxonomy/**
 
+krona/ktimporttext:
+  - modules/krona/ktimporttext/**
+  - tests/modules/krona/ktimporttext/**
+
 last/dotplot:
   - modules/last/dotplot/**
   - tests/modules/last/dotplot/**
@@ -1599,6 +1607,10 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
+samtools/bamtocram:
+  - modules/samtools/bamtocram/**
+  - tests/modules/samtools/bamtocram/**
+
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
   - tests/modules/samtools/collatefastq/**

tests/config/test_data.config

@@ -14,6 +14,7 @@ params {
                 genome_paf                                     = "${test_data_dir}/genomics/sarscov2/genome/genome.paf"
                 genome_sizes                                   = "${test_data_dir}/genomics/sarscov2/genome/genome.sizes"
                 transcriptome_fasta                            = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.fasta"
+                proteome_fasta                                 = "${test_data_dir}/genomics/sarscov2/genome/proteome.fasta"
                 transcriptome_paf                              = "${test_data_dir}/genomics/sarscov2/genome/transcriptome.paf"
 
                 test_bed                                       = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed"
@@ -109,6 +110,9 @@ params {
 
                 test_sequencing_summary                        = "${test_data_dir}/genomics/sarscov2/nanopore/sequencing_summary/test.sequencing_summary.txt"
             }
+            'metagenome' {
+                kraken_report                                  = "${test_data_dir}/genomics/sarscov2/metagenome/test_1.kraken2.report.txt"
+            }
         }
         'homo_sapiens' {
             'genome' {
@@ -245,8 +249,8 @@ params {
                 test2_2_fastq_gz                               = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
                 test2_umi_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
                 test2_umi_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
-                test_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_1.fastq.gz"
+                test_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
-                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
+                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
 
                 test_baserecalibrator_table                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
                 test2_baserecalibrator_table                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"

tests/modules/antismash/antismashlitedownloaddatabases/test.yml

@@ -1,14 +1,17 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash/antismashlitedownloaddatabases
     - antismash
+    - antismash/antismashlitedownloaddatabases
   files:
     - path: output/antismash/versions.yml
-      md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
+      md5sum: 24859c67023abab99de295d3675a24b6
     - path: output/antismash/antismash_db
     - path: output/antismash/antismash_db/clusterblast
     - path: output/antismash/antismash_db/clustercompare
     - 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

tests/modules/bamtools/split/main.nf

@@ -2,13 +2,29 @@
 
 nextflow.enable.dsl = 2
 
-include { BAMTOOLS_SPLIT } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_SINGLE   } from '../../../../modules/bamtools/split/main.nf'
+include { BAMTOOLS_SPLIT as BAMTOOLS_SPLIT_MULTIPLE } from '../../../../modules/bamtools/split/main.nf'
 
-workflow test_bamtools_split {
+workflow test_bamtools_split_single_input {
 
     input = [
         [ id:'test', single_end:false ], // 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'], checkIfExists: true)
+    ]
 
-    BAMTOOLS_SPLIT ( input )
+    BAMTOOLS_SPLIT_SINGLE ( input )
 }
+
+workflow test_bamtools_split_multiple {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+        ]
+    ]
+
+    BAMTOOLS_SPLIT_MULTIPLE ( input )
+}
+

tests/modules/bamtools/split/test.yml

@@ -1,10 +1,23 @@
-- name: bamtools split test_bamtools_split
+- name: bamtools split test_bamtools_split_single_input
-  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_single_input -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
   tags:
-    - bamtools/split
     - bamtools
+    - bamtools/split
   files:
-    - path: output/bamtools/test.paired_end.sorted.REF_chr22.bam
+    - path: output/bamtools/test.REF_chr22.bam
       md5sum: b7dc50e0edf9c6bfc2e3b0e6d074dc07
-    - path: output/bamtools/test.paired_end.sorted.REF_unmapped.bam
+    - path: output/bamtools/test.REF_unmapped.bam
       md5sum: e0754bf72c51543b2d745d96537035fb
+    - path: output/bamtools/versions.yml
+
+- name: bamtools split test_bamtools_split_multiple
+  command: nextflow run ./tests/modules/bamtools/split -entry test_bamtools_split_multiple -c ./tests/config/nextflow.config -c ./tests/modules/bamtools/split/nextflow.config
+  tags:
+    - bamtools
+    - bamtools/split
+  files:
+    - path: output/bamtools/test.REF_chr22.bam
+      md5sum: 585675bea34c48ebe9db06a561d4b4fa
+    - path: output/bamtools/test.REF_unmapped.bam
+      md5sum: 16ad644c87b9471f3026bc87c98b4963
+    - path: output/bamtools/versions.yml

tests/modules/diamond/blastp/main.nf

@@ -7,9 +7,22 @@ include { DIAMOND_BLASTP } from '../../../../modules/diamond/blastp/main.nf'
 
 workflow test_diamond_blastp {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    out_ext = 'txt'
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
+
+workflow test_diamond_blastp_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    out_ext = 'daa'
+    blast_columns = []
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTP ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }

tests/modules/diamond/blastp/test.yml

@@ -1,8 +1,17 @@
-- name: diamond blastp
+- name: diamond blastp test_diamond_blastp
-  command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config
+  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp -c tests/config/nextflow.config
   tags:
-    - diamond
     - diamond/blastp
+    - diamond
   files:
-    - path: ./output/diamond/test.diamond_blastp.txt
+    - path: output/diamond/test.diamond_blastp.txt
-      md5sum: 3ca7f6290c1d8741c573370e6f8b4db0
+    - path: output/diamond/versions.yml
+
+- name: diamond blastp test_diamond_blastp_daa
+  command: nextflow run tests/modules/diamond/blastp -entry test_diamond_blastp_daa -c tests/config/nextflow.config
+  tags:
+    - diamond/blastp
+    - diamond
+  files:
+    - path: output/diamond/test.diamond_blastp.daa
+    - path: output/diamond/versions.yml

tests/modules/diamond/blastx/main.nf

@@ -7,9 +7,22 @@ include { DIAMOND_BLASTX } from '../../../../modules/diamond/blastx/main.nf'
 
 workflow test_diamond_blastx {
 
-    db = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
     fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    out_ext = 'tfdfdt'  // Nonsense file extension to check default case.
+    blast_columns = 'qseqid qlen'
 
     DIAMOND_MAKEDB ( db )
-    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
+}
+
+workflow test_diamond_blastx_daa {
+
+    db = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
+    fasta = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+    out_ext = 'daa'
+    blast_columns = []
+
+    DIAMOND_MAKEDB ( db )
+    DIAMOND_BLASTX ( [ [id:'test'], fasta ], DIAMOND_MAKEDB.out.db, out_ext, blast_columns )
 }

tests/modules/diamond/blastx/test.yml

@@ -1,8 +1,18 @@
-- name: diamond blastx
+- name: diamond blastx test_diamond_blastx
-  command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config
+  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx -c tests/config/nextflow.config
   tags:
     - diamond
     - diamond/blastx
   files:
-    - path: ./output/diamond/test.diamond_blastx.txt
+    - path: output/diamond/test.diamond_blastx.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/diamond/versions.yml
+
+- name: diamond blastx test_diamond_blastx_daa
+  command: nextflow run tests/modules/diamond/blastx -entry test_diamond_blastx_daa -c tests/config/nextflow.config
+  tags:
+    - diamond
+    - diamond/blastx
+  files:
+    - path: output/diamond/test.diamond_blastx.daa
+      md5sum: 0df4a833408416f32981415873facc11
+    - path: output/diamond/versions.yml

tests/modules/diamond/makedb/main.nf

@@ -6,7 +6,7 @@ include { DIAMOND_MAKEDB } from '../../../../modules/diamond/makedb/main.nf'
 
 workflow test_diamond_makedb {
 
-    input = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+    input = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
 
     DIAMOND_MAKEDB ( input )
 }

tests/modules/diamond/makedb/test.yml

@@ -1,8 +1,9 @@
 - name: diamond makedb test_diamond_makedb
-  command: nextflow run ./tests/modules/diamond/makedb -entry test_diamond_makedb -c ./tests/config/nextflow.config -c ./tests/modules/diamond/makedb/nextflow.config
+  command: nextflow run tests/modules/diamond/makedb -entry test_diamond_makedb -c tests/config/nextflow.config
   tags:
-    - diamond
     - diamond/makedb
+    - diamond
   files:
-    - path: output/diamond/genome.fasta.dmnd
+    - path: output/diamond/proteome.fasta.dmnd
-      md5sum: 2447fb376394c20d43ea3aad2aa5d15d
+      md5sum: fc28c50b202dd7a7c5451cddff2ba1f4
+    - path: output/diamond/versions.yml

tests/modules/elprep/merge/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ELPREP_SPLIT } from '../../../../modules/elprep/split/main.nf'
+include { ELPREP_MERGE } from '../../../../modules/elprep/merge/main.nf'
+
+workflow test_elprep_merge {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    ]
+
+    ELPREP_SPLIT ( input )
+    ELPREP_MERGE ( ELPREP_SPLIT.out.bam )
+}

tests/modules/elprep/merge/nextflow.config

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

tests/modules/elprep/merge/test.yml

@@ -0,0 +1,8 @@
+- name: elprep merge test_elprep_merge
+  command: nextflow run tests/modules/elprep/merge -entry test_elprep_merge -c tests/config/nextflow.config
+  tags:
+    - elprep
+    - elprep/merge
+  files:
+    - path: output/elprep/output/test.bam
+    - path: output/elprep/versions.yml

tests/modules/gatk4/splitncigarreads/main.nf

@@ -6,7 +6,23 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarre
 
 workflow test_gatk4_splitncigarreads {
     input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                [],
+                []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_splitncigarreads_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)

tests/modules/gatk4/splitncigarreads/test.yml

@@ -5,5 +5,14 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: ceed15c0bd64ff5c38d3816905933b0b
+      md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
+    - path: output/gatk4/versions.yml
+- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
+  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/splitncigarreads
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: cd56e3225950f519fd47164cca60a0bb
     - path: output/gatk4/versions.yml

tests/modules/krona/ktimporttext/main.nf

@@ -0,0 +1,31 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KRONA_KTIMPORTTEXT } from '../../../../modules/krona/ktimporttext/main.nf'
+
+workflow test_krona_ktimporttext_multi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/ktimporttext.txt', checkIfExists: true), // krona default test file
+            file(params.test_data['sarscov2']['metagenome']['kraken_report'], checkIfExists: true), //Kraken2 report file
+            file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/krona/kaiju_out4krona.txt', checkIfExists: true) // Kaiju output 4 krona
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}
+
+workflow test_krona_ktimporttext_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file('http://krona.sourceforge.net/examples/text.txt', checkIfExists: true) // krona default test file
+        ]
+    ]
+
+    KRONA_KTIMPORTTEXT ( input )
+}

tests/modules/krona/ktimporttext/nextflow.config

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

tests/modules/krona/ktimporttext/test.yml

@@ -0,0 +1,19 @@
+- name: krona ktimporttext test_krona_ktimporttext_multi
+  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_multi -c tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"
+
+- name: krona ktimporttext test_krona_ktimporttext_single
+  command: nextflow run tests/modules/krona/ktimporttext -entry test_krona_ktimporttext_single -c tests/config/nextflow.config
+  tags:
+    - krona
+    - krona/ktimporttext
+  files:
+    - path: output/krona/test.html
+      contains:
+        - "DOCTYPE html PUBLIC"

tests/modules/minimap2/align/main.nf

@@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
 }
 
 workflow test_minimap2_align_paired_end {
@@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format  = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
 }

tests/modules/minimap2/align/test.yml

@@ -1,17 +1,17 @@
-- name: minimap2 align single-end
+- name: minimap2 align test_minimap2_align_single_end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
+    - path: output/minimap2/test.bam
-      md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
+    - path: output/minimap2/versions.yml
 
-- name: minimap2 align paired-end
+- name: minimap2 align test_minimap2_align_paired_end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
+    - path: output/minimap2/test.bam
-      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
+    - path: output/minimap2/versions.yml

tests/modules/picard/addorreplacereadgroups/test.yml

@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 7b82f3461c2d80fc6a10385e78c9427f
     - path: output/picard/versions.yml
-      md5sum: 8a2d176295e1343146ea433c79bb517f

tests/modules/picard/cleansam/test.yml

@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: a48f8e77a1480445efc57570c3a38a68
     - path: output/picard/versions.yml
-      md5sum: e6457d7c6de51bf6f4b577eda65e57ac

tests/modules/picard/collectwgsmetrics/main.nf

@@ -7,7 +7,6 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
 workflow test_picard_collectwgsmetrics {
     input = [ [ id:'test', single_end:false ], // meta map
             file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 

tests/modules/picard/createsequencedictionary/test.yml

@@ -7,4 +7,3 @@
     - path: output/picard/test.dict
       contains: ["SN:MT192765.1"]
     - path: output/picard/versions.yml
-      md5sum: b3d8c7ea65b8a6d3237b153d13fe2014

tests/modules/picard/fixmateinformation/test.yml

@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 746102e8c242c0ef42e045c49d320030
     - path: output/picard/versions.yml
-      md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb

tests/modules/picard/liftovervcf/nextflow.config

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

tests/modules/picard/markduplicates/nextflow.config

@@ -3,7 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: PICARD_MARKDUPLICATES_UNSORTED {
-        ext.args = 'ASSUME_SORT_ORDER=queryname'
+        ext.args = '--ASSUME_SORT_ORDER queryname'
     }
 
 }

tests/modules/rsem/calculateexpression/test.yml

@@ -42,7 +42,7 @@
     - path: output/rsem/rsem/genome.transcripts.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29
     - path: output/rsem/rsem/genomeParameters.txt
-      md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f
+      md5sum: df5a456e3242520cc36e0083a6a7d9dd
     - path: output/rsem/rsem/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
     - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
@@ -63,4 +63,4 @@
     - path: output/rsem/test.stat/test.theta
       md5sum: de2e4490c98cc5383a86ae8225fd0a28
     - path: output/rsem/test.transcript.bam
-      md5sum: 7846491086c478858419667d60f18edd
+      md5sum: ed681d39f5700ffc74d6321525330d93

tests/modules/samtools/bamtocram/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
+
+workflow test_samtools_bamtocram {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
+}

tests/modules/samtools/bamtocram/nextflow.config

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

tests/modules/samtools/bamtocram/test.yml

@@ -0,0 +1,9 @@
+- name: samtools bamtocram test_samtools_bamtocram
+  command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
+  tags:
+    - samtools/bamtocram
+    - samtools
+  files:
+    - path: output/samtools/test.cram
+    - path: output/samtools/test.cram.crai
+    - path: output/samtools/versions.yml

tests/modules/tabix/tabix/main.nf

@@ -4,7 +4,8 @@ nextflow.enable.dsl = 2
 
 include { TABIX_TABIX as TABIX_BED     } from '../../../../modules/tabix/tabix/main.nf'
 include { TABIX_TABIX as TABIX_GFF     } from '../../../../modules/tabix/tabix/main.nf'
-include { TABIX_TABIX as TABIX_VCF } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_TBI } from '../../../../modules/tabix/tabix/main.nf'
+include { TABIX_TABIX as TABIX_VCF_CSI } from '../../../../modules/tabix/tabix/main.nf'
 
 workflow test_tabix_tabix_bed {
     input = [ [ id:'B.bed' ], // meta map
@@ -22,10 +23,18 @@ workflow test_tabix_tabix_gff {
     TABIX_GFF ( input )
 }
 
-workflow test_tabix_tabix_vcf {
+workflow test_tabix_tabix_vcf_tbi {
     input = [ [ id:'test.vcf' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ] 
             ]
 
-    TABIX_VCF ( input )
+    TABIX_VCF_TBI ( input )
+}
+
+workflow test_tabix_tabix_vcf_csi {
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+            ]
+
+    TABIX_VCF_CSI ( input )
 }

tests/modules/tabix/tabix/nextflow.config

@@ -10,8 +10,12 @@ process {
         ext.args = '-p gff'
     }
 
-    withName: TABIX_VCF {
+    withName: TABIX_VCF_TBI {
         ext.args = '-p vcf'
     }
 
+   withName: TABIX_VCF_CSI {
+        ext.args = '-p vcf --csi'
+    }
+
 }

tests/modules/tabix/tabix/test.yml

@@ -15,10 +15,18 @@
     - path: ./output/tabix/genome.gff3.gz.tbi
       md5sum: f79a67d95a98076e04fbe0455d825926
 - name: tabix tabix vcf
-  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_tbi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
   tags:
     - tabix
     - tabix/tabix
   files:
     - path: output/tabix/test.vcf.gz.tbi
       md5sum: 36e11bf96ed0af4a92caa91a68612d64
+- name: tabix tabix vcf csi
+  command: nextflow run ./tests/modules/tabix/tabix -entry test_tabix_tabix_vcf_csi -c ./tests/config/nextflow.config -c ./tests/modules/tabix/tabix/nextflow.config
+  tags:
+    - tabix
+    - tabix/tabix
+  files:
+    - path: output/tabix/test.vcf.gz.csi
+      md5sum: 5f930522d2b9dcdba2807b7da4dfa3fd

tests/modules/tiddit/sv/test.yml

@@ -9,6 +9,7 @@
     - path: output/tiddit/test.signals.tab
       md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
+      md5sum: bdce14ae8292bf3deb81f6f255baf859
 
 - name: tiddit sv no ref
   command: nextflow run ./tests/modules/tiddit/sv -entry test_tiddit_sv_no_ref -c ./tests/config/nextflow.config -c ./tests/modules/tiddit/sv/nextflow.config
@@ -21,3 +22,4 @@
     - path: output/tiddit/test.signals.tab
       md5sum: dab4b2fec4ddf8eb1c23005b0770150e
     - path: output/tiddit/test.vcf
+      md5sum: 3d0e83a8199b2bdb81cfe3e6b12bf64b

tests/subworkflows/nf-core/bam_qc_picard/main.nf

@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/main' addParams([:])
+
+workflow test_bam_qc_picard_wgs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    BAM_QC_PICARD ( input, fasta, fasta_fai, [], [] )
+}
+
+workflow test_bam_qc_picard_targetted {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bait        = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target      = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    BAM_QC_PICARD ( input, fasta, fasta_fai, bait, target )
+}

tests/subworkflows/nf-core/bam_qc_picard/nextflow.config

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

tests/subworkflows/nf-core/bam_qc_picard/test.yml

@@ -0,0 +1,33 @@
+- name: bam qc picard wgs
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_wgs -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collectwgsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test.CollectWgsMetrics.coverage_metrics
+
+- name: bam qc picard targetted
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_targetted -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collecthsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test.CollectHsMetrics.coverage_metrics