Merge branch 'master' into rp3-add-shigatyper

2024-11-10 20:23:10 +00:00 · 2022-04-28 09:51:36 -06:00 · 2022-04-28 09:51:36 -06:00 · 4b6ee6fc14
commit 4b6ee6fc14
parent 30bd93602f b3e9b88e80
18 changed files with 191 additions and 20 deletions
--- a/modules/gatk4/haplotypecaller/main.nf
+++ b/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:
--- a/modules/krona/ktimporttext/main.nf
+++ b/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
+    """
+}
--- a/modules/krona/ktimporttext/meta.yml
+++ b/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"
--- a/modules/rsem/calculateexpression/main.nf
+++ b/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' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"

    input:
    tuple val(meta), path(reads)
--- a/modules/rsem/preparereference/main.nf
+++ b/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' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"

    input:
    path fasta, stageAs: "rsem/*"
--- a/modules/tabix/tabix/main.nf
+++ b/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:
--- a/modules/tabix/tabix/meta.yml
+++ b/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
--- a/modules/tiddit/sv/main.nf
+++ b/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 \\
--- a/tests/config/pytest_modules.yml
+++ b/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/**
--- a/tests/config/test_data.config
+++ b/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' {
@ -245,8 +248,8 @@ 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_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
+                test_rnaseq_1_fastq_gz                         = "${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_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"
--- a/tests/modules/krona/ktimporttext/main.nf
+++ b/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 )
+}
--- a/tests/modules/krona/ktimporttext/nextflow.config
+++ b/tests/modules/krona/ktimporttext/nextflow.config
@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
--- a/tests/modules/krona/ktimporttext/test.yml
+++ b/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"
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ b/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
--- a/tests/modules/tabix/tabix/main.nf
+++ b/tests/modules/tabix/tabix/main.nf
@ -2,9 +2,10 @@

 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_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_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 )
 }
--- a/tests/modules/tabix/tabix/nextflow.config
+++ b/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'
+    }
+
 }
--- a/tests/modules/tabix/tabix/test.yml
+++ b/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
--- a/tests/modules/tiddit/sv/test.yml
+++ b/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