Merge branch 'master' into bat-test

.github/workflows/pytest-workflow.yml

@@ -48,11 +48,6 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-pip-
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pytest-workflow
 
@@ -96,13 +91,8 @@ jobs:
       - name: Output log on failure
         if: failure()
         run: |
-          sudo apt install bat
+          sudo apt install -qq bat
-          echo "======> log.out <======="
+          bat /home/runner/pytest_workflow_*/*/log.{out,err}          
-          bat /home/runner/pytest_workflow_*/*/log.out
-          echo
-          echo
-          echo "======> log.err <======="
-          bat /home/runner/pytest_workflow_*/*/log.err
 
       - name: Upload logs on failure
         if: failure()

modules/chromap/chromap/main.nf

@@ -1,13 +1,11 @@
-def VERSION = '0.1' // Version information not provided by tool on CLI
-
 process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::chromap=0.1 bioconda::samtools=1.13" : null)
+    conda (params.enable_conda ? "bioconda::chromap=0.1.5 bioconda::samtools=1.14" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:2cad7c5aa775241887eff8714259714a39baf016-0' }"
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:724a1037d59f6a19c9d4e7bdba77b52b37de0dc3-0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -45,7 +43,7 @@ process CHROMAP_CHROMAP {
         args_list << "--pairs-natural-chr-order $pairs_chr_order"
     }
     def final_args = args_list.join(' ')
-    def compression_cmds = "gzip ${prefix}.${file_extension}"
+    def compression_cmds = "gzip -n ${prefix}.${file_extension}"
     if (args.contains("--SAM")) {
         compression_cmds = """
         samtools view $args2 -@ $task.cpus -bh \\
@@ -67,7 +65,8 @@ process CHROMAP_CHROMAP {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            chromap: $VERSION
+            chromap: \$(echo \$(chromap --version 2>&1))
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     } else {
@@ -85,7 +84,8 @@ process CHROMAP_CHROMAP {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            chromap: $VERSION
+            chromap: \$(echo \$(chromap --version 2>&1))
+            samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
         END_VERSIONS
         """
     }

modules/vcfanno/main.nf

@@ -0,0 +1,34 @@
+process VCFANNO {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::vcfanno=0.3.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcfanno:0.3.3--h9ee0642_0':
+        'quay.io/biocontainers/vcfanno:0.3.3--h9ee0642_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    path vcfanno_config
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf
+    path "versions.yml"           , emit: versions
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    vcfanno \\
+        -p $task.cpus \\
+        $args \\
+        $vcfanno_config \\
+        $vcf \\
+        > ${prefix}_annotated.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
+    END_VERSIONS
+    """
+}

modules/vcfanno/meta.yml

@@ -0,0 +1,56 @@
+name: vcfanno
+description: quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files
+keywords:
+  - vcf
+  - bed
+  - annotate
+  - variant
+tools:
+  - vcfanno:
+      description: annotate a VCF with other VCFs/BEDs/tabixed files
+      homepage: None
+      documentation: https://github.com/brentp/vcfanno#vcfanno
+      tool_dev_url: https://github.com/brentp/vcfanno
+      doi: "10.1186/s13059-016-0973-5"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: query VCF file
+      pattern: "*.{vcf.gz}"
+  - vcf.tbi:
+      type: file
+      description: query VCF file index
+      pattern: "*.{vcf.gz.tbi}"
+  - vcfanno_config:
+      type: file
+      description: |
+        A simple configuration file is used to specify both the source files
+        and the set of attributes (in the case of VCF)
+        or columns (in the case of BED or other tab-delimited formats)
+        that should be added to the query file.
+      pattern: "*.{toml}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: Annotated VCF file
+      pattern: "*.{vcf}"
+
+authors:
+  - "@projectoriented"

tests/config/pytest_modules.yml

@@ -1493,6 +1493,10 @@ variantbam:
   - modules/variantbam/**
   - tests/modules/variantbam/**
 
+vcfanno:
+  - modules/vcfanno/**
+  - tests/modules/vcfanno/**
+
 vcflib/vcfuniq:
   - modules/vcflib/vcfuniq/**
   - tests/modules/vcflib/vcfuniq/**

tests/modules/chromap/chromap/test.yml

@@ -5,9 +5,8 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bed.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: 25e40bde24c7b447292cd68573728694
 
 - name: chromap chromap test_chromap_chromap_paired_end
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -16,9 +15,8 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bed.gz
-      md5sum: cafd8fb21977f5ae69e9008b220ab169
+      md5sum: 7cdc8448882b75811e0c784f5f20aef2
 
 - name: chromap chromap test_chromap_chromap_paired_bam
   command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@@ -27,6 +25,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
-      md5sum: f889d5f61d80823766af33277d27d386
     - path: output/chromap/test.bam
-      md5sum: bd1e3fe0f3abd1430ae191754f16a3ed
+      md5sum: 73e2c76007e3c61df625668e01b3f42f

tests/modules/chromap/index/test.yml

@@ -5,3 +5,5 @@
     - chromap
   files:
     - path: output/chromap/genome.index
+
+

tests/modules/vcfanno/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFANNO } from '../../../modules/vcfanno/main.nf'
+
+workflow test_vcfanno {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
+    ]
+
+    toml = file("https://raw.githubusercontent.com/nf-core/test-datasets/8fbd9f99a2feb3f9e39cd3bcdc4a9176a5835673/data/delete_me/vcfanno.toml", 
+                checkIfExists: true)
+
+    VCFANNO ( input, toml )
+}

tests/modules/vcfanno/nextflow.config

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

tests/modules/vcfanno/test.yml

@@ -0,0 +1,9 @@
+- name: vcfanno test_vcfanno
+  command: nextflow run tests/modules/vcfanno -entry test_vcfanno -c tests/config/nextflow.config
+  tags:
+    - vcfanno
+  files:
+    - path: output/vcfanno/test_annotated.vcf
+      md5sum: 34259cf6b0a4698a2917ad3554b50c0f
+    - path: output/vcfanno/versions.yml
+      md5sum: 62d13540503b22f04a2280c91942cb03