Merge branch 'master' into subwf/bam_qc

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/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 \\

tests/config/pytest_modules.yml

@@ -1050,6 +1050,10 @@ 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/**

tests/config/test_data.config

@@ -109,6 +109,9 @@ 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' {

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/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