New module: instrain/compare (#3623)

* Started instrain compare tests * instrain compare * Update modules/nf-core/instrain/compare/main.nf * Update modules/nf-core/instrain/compare/main.nf * Update modules/nf-core/instrain/compare/main.nf * Updated test.yml and added stub * Update modules/nf-core/instrain/compare/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update meta.yml to include meta2 * Updated test.yml output files * Changed md5 to content for several test.yml files * changed content to contains * Added another contains option in test.yml * shortened contains string to pass prettier check --------- Co-authored-by: Margot Lavitt <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]>
nf-core · Jul 19, 2023 · 7f39bf3 · 7f39bf3
1 parent 8c029dd
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diff --git a/modules/nf-core/instrain/compare/main.nf b/modules/nf-core/instrain/compare/main.nf
@@ -0,0 +1,57 @@
+process INSTRAIN_COMPARE {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "bioconda::instrain=1.6.1"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/instrain:1.6.1--pyhdfd78af_0':
+        'biocontainers/instrain:1.6.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(profiles)
+    tuple val(meta2), path(bams)
+    path stb_file
+
+    output:
+    tuple val(meta), path("*.IS_compare")   , emit: compare
+    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 stb_args = stb_file ? "-s ${stb_file}": ''
+    """
+    inStrain \\
+        compare \\
+        -i $profiles \\
+        -o ${prefix}.IS_compare \\
+        --processes $task.cpus \\
+        --bams $bams \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        instrain: \$(echo \$(inStrain compare --version 2>&1) | awk 'NF{ print \$NF }')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def stb_args = stb_file ? "-s ${stb_file}": ''
+    """
+    mkdir -p ${prefix}.IS_compare/output
+    touch ${prefix}.IS_compare/output/${prefix}.IS_compare_pooled_SNV_info.tsv
+    touch ${prefix}.IS_compare/output/${prefix}.IS_compare_comparisonsTable.tsv
+    touch ${prefix}.IS_compare/output/${prefix}.IS_compare_pooled_SNV_data.tsv
+    touch ${prefix}.IS_compare/output/${prefix}.IS_compare_pooled_SNV_data_keys.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        instrain: \$(echo \$(inStrain compare --version 2>&1) | awk 'NF{ print \$NF }')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/instrain/compare/meta.yml b/modules/nf-core/instrain/compare/meta.yml
@@ -0,0 +1,59 @@
+name: "instrain_compare"
+description: Strain-level comparisons across multiple inStrain profiles
+keywords:
+  - instrain
+  - compare
+  - align
+  - diversity
+  - coverage
+tools:
+  - "instrain":
+      description: "Calculation of strain-level metrics"
+      homepage: https://github.com/MrOlm/instrain
+      documentation: https://instrain.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/MrOlm/instrain
+      doi: 10.1038/s41587-020-00797-0
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  - profiles:
+      type: directory
+      description: InStrain profile folders
+      pattern: "*.IS/"
+  - bams:
+      type: file
+      description: Path to .bam files that were profiled
+      pattern: "*.{bam,sam}"
+  - stb_file:
+      type: file
+      description: Path to .stb (scaffold to bin) file that was profiled
+      pattern: "*.stb"
+
+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"
+  - compare:
+      type: directory
+      description: inStrain compare folders
+      pattern: "*.IS_compare/"
+
+authors:
+  - "@margotl9"
+  - "@CarsonJM"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1929,6 +1929,10 @@ ilastik/pixelclassification:
   - modules/nf-core/ilastik/pixelclassification/**
   - tests/modules/nf-core/ilastik/pixelclassification/**
 
+instrain/compare:
+  - modules/nf-core/instrain/compare/**
+  - tests/modules/nf-core/instrain/compare/**
+
 instrain/profile:
   - modules/nf-core/instrain/profile/**
   - tests/modules/nf-core/instrain/profile/**

diff --git a/tests/modules/nf-core/instrain/compare/main.nf b/tests/modules/nf-core/instrain/compare/main.nf
@@ -0,0 +1,22 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { INSTRAIN_COMPARE } from '../../../../../modules/nf-core/instrain/compare/main.nf'
+include { INSTRAIN_PROFILE } from '../../../../../modules/nf-core/instrain/profile/main.nf'
+
+workflow test_instrain_compare {
+
+     input = Channel.of(
+        [[ id:'test1', single_end:true ], file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
+        [[ id:'test2', single_end:true ], file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)]
+    )
+    genome_fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+
+    INSTRAIN_PROFILE ( input , genome_fasta , [] , [] )
+    instrain_profiles = INSTRAIN_PROFILE.out.profile.map{ [[id:"test"], it[1]] }.groupTuple()
+    input_bams = input.map{ [[id:"test"], it[1]] }.groupTuple()
+
+    INSTRAIN_COMPARE ( instrain_profiles , input_bams , [] )
+
+}
diff --git a/tests/modules/nf-core/instrain/compare/nextflow.config b/tests/modules/nf-core/instrain/compare/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/nf-core/instrain/compare/test.yml b/tests/modules/nf-core/instrain/compare/test.yml
@@ -0,0 +1,27 @@
+- name: instrain compare test_instrain_compare
+  command: nextflow run ./tests/modules/nf-core/instrain/compare -entry test_instrain_compare -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/instrain/compare/nextflow.config
+  tags:
+    - instrain
+    - instrain/compare
+  files:
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_comparisonsTable.tsv
+      contains: ["test2.paired_end.sorted.bam	0.9516129032258064	944	0.0235994100147496	40001	0	0	1.0	1.0"]
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_data.tsv
+      contains: ["0	1981	119	0	0	24"]
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_data_keys.tsv
+      contains: ["paired_end.sorted.bam	chr22"]
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_info.tsv
+      md5sum: 7ed4894afbc4f1abd8692c4a65003a27
+    - path: output/instrain/versions.yml
+
+- name: instrain compare test_instrain_compare_stub
+  command: nextflow run ./tests/modules/nf-core/instrain/compare -entry test_instrain_compare -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/instrain/compare/nextflow.config -stub-run
+  tags:
+    - instrain
+    - instrain/compare
+  files:
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_comparisonsTable.tsv
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_data.tsv
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_data_keys.tsv
+    - path: output/instrain/test.IS_compare/output/test.IS_compare_pooled_SNV_info.tsv
+    - path: output/instrain/versions.yml