diff --git a/modules/nf-core/picrust2/pipeline/environment.yml b/modules/nf-core/picrust2/pipeline/environment.yml new file mode 100644 index 00000000000..ab6df7c1029 --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::picrust2=2.6.2" diff --git a/modules/nf-core/picrust2/pipeline/main.nf b/modules/nf-core/picrust2/pipeline/main.nf new file mode 100644 index 00000000000..86d92c3a63c --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/main.nf @@ -0,0 +1,63 @@ +process PICRUST2_PIPELINE { + tag "${meta.id}" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6a/6a9b732fec49b33334dcff4f8875dcd552402ead5654443a54c7f4f79823df78/data' + : 'community.wave.seqera.io/library/picrust2:2.6.2--a7c158f7c987b452'}" + + input: + tuple val(meta), path(sequences), path(otu_table) + + output: + tuple val(meta), path("${prefix}/") , emit: output_dir + tuple val(meta), path("${prefix}/*_reduced.tre") , emit: trees + tuple val(meta), path("${prefix}_metagenome_*_abundances.tsv.gz"), emit: function_abundances + tuple val(meta), path("${prefix}_pathway_abundances.tsv.gz") , emit: pathway_abundances + path 'versions.yml', emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + picrust2_pipeline.py \\ + --study_fasta ${sequences} \\ + --input ${otu_table} \\ + --processes ${task.cpus} \\ + --output ${prefix} \\ + ${args} + + cp ${prefix}/pathways_out/path_abun_unstrat.tsv.gz ${prefix}_pathway_abundances.tsv.gz + + for metagenome_dir in ${prefix}/*_metagenome_out; do + func_type=\$(basename \$metagenome_dir _metagenome_out) + cp \${metagenome_dir}/pred_metagenome_unstrat.tsv.gz ${prefix}_metagenome_\${func_type}_abundances.tsv.gz + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picrust2: \$( picrust2_pipeline.py --version | sed 's/PICRUSt2 //' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo ${args} + + mkdir -p ${prefix} + touch ${prefix}/bac_reduced.tre + echo '' | gzip -c > ${prefix}_metagenome_EC_abundances.tsv.gz + echo '' | gzip -c > ${prefix}_pathway_abundances.tsv.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + picrust2: \$( picrust2_pipeline.py --version | sed 's/PICRUSt2 //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/picrust2/pipeline/meta.yml b/modules/nf-core/picrust2/pipeline/meta.yml new file mode 100644 index 00000000000..313562c6a11 --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/meta.yml @@ -0,0 +1,97 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "picrust2_pipeline" +description: Predict metagenome functional content from marker gene sequences + and OTU/ASV abundance data +keywords: + - metagenomics + - functional prediction + - 16S + - microbiome +tools: + - "picrust2": + description: "PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction + of Unobserved States" + homepage: "https://github.com/picrust/picrust2/wiki" + documentation: "https://github.com/picrust/picrust2/wiki" + tool_dev_url: "https://github.com/picrust/picrust2" + doi: "10.1038/s41587-020-0548-6" + licence: ["GPL v3"] + identifier: biotools:picrust2 + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - sequences: + type: file + description: FASTA file containing study sequences (e.g., 16S rRNA + sequences) + pattern: "*.{fasta,fa,fna}" + ontologies: [] + - otu_table: + type: file + description: OTU/ASV abundance table in BIOM or TSV format + pattern: "*.{biom,tsv,txt}" + + ontologies: + - edam: http://edamontology.org/format_3746 # BIOM format + - edam: http://edamontology.org/format_3475 # TSV +output: + output_dir: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}/: + type: directory + description: Complete output directory of PICRUSt2 pipeline + trees: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}/*_reduced.tre: + type: file + description: Phylogenetic trees with reduced marker gene sequences + pattern: "*_reduced.tre" + ontologies: [] + function_abundances: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}/*_metagenome_out/pred_metagenome_unstrat.tsv.gz: + type: file + description: Predicted metagenome functional abundances (unstratified) + pattern: "pred_metagenome_unstrat.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + pathway_abundances: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}/pathways_out/path_abun_unstrat.tsv.gz: + type: file + description: Predicted pathway abundances (unstratified) + pattern: "path_abun_unstrat.tsv.gz" + ontologies: + - edam: http://edamontology.org/format_3989 # GZIP format + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: "http://edamontology.org/format_3750" # YAML + +authors: + - "@dialvarezs" +maintainers: + - "@dialvarezs" diff --git a/modules/nf-core/picrust2/pipeline/tests/main.nf.test b/modules/nf-core/picrust2/pipeline/tests/main.nf.test new file mode 100644 index 00000000000..5e754f349b5 --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/tests/main.nf.test @@ -0,0 +1,75 @@ +nextflow_process { + + name "Test Process PICRUST2_PIPELINE" + script "../main.nf" + process "PICRUST2_PIPELINE" + + tag "modules" + tag "modules_nfcore" + tag "picrust2" + tag "picrust2/pipeline" + + + test("picrust2 pipeline [16s otu]") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'metabarcoding/16S_OTU/rep-seq.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'metabarcoding/16S_OTU/feature-table.tsv', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.trees, + process.out.function_abundances, + process.out.pathway_abundances + ).match() }, + { assert snapshot( + path(process.out.versions.get(0)).yaml + ).match("versions") } + ) + } + + } + + test("picrust2 pipeline [16s otu] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'metabarcoding/16S_OTU/rep-seq.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'metabarcoding/16S_OTU/feature-table.tsv', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.trees, + process.out.function_abundances, + process.out.pathway_abundances, + path(process.out.versions.get(0)).yaml + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/picrust2/pipeline/tests/main.nf.test.snap b/modules/nf-core/picrust2/pipeline/tests/main.nf.test.snap new file mode 100644 index 00000000000..5a7fcb2e1b4 --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/tests/main.nf.test.snap @@ -0,0 +1,90 @@ +{ + "picrust2 pipeline [16s otu] - stub": { + "content": [ + [ + [ + { + "id": "test" + }, + "bac_reduced.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test" + }, + "test_metagenome_EC_abundances.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + [ + [ + { + "id": "test" + }, + "test_pathway_abundances.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + { + "PICRUST2_PIPELINE": { + "picrust2": "2.6.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-23T09:22:34.879189621" + }, + "versions": { + "content": [ + { + "PICRUST2_PIPELINE": { + "picrust2": "2.6.2" + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-21T05:16:14.5417447" + }, + "picrust2 pipeline [16s otu]": { + "content": [ + [ + [ + { + "id": "test" + }, + [ + "arc_reduced.tre:md5,35617cfa837738468b8e6a15b6bc8795", + "bac_reduced.tre:md5,72049e7bc0531b9d55771481cb970883" + ] + ] + ], + [ + [ + { + "id": "test" + }, + "test_metagenome_EC_abundances.tsv.gz:md5,b4e292e86ec6f663c8d3ece1c5f47eb9" + ] + ], + [ + [ + { + "id": "test" + }, + "test_pathway_abundances.tsv.gz:md5,632c0078254a10e6518e2ae6019b5f17" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.8" + }, + "timestamp": "2025-10-23T09:22:29.693722206" + } +} \ No newline at end of file diff --git a/modules/nf-core/picrust2/pipeline/tests/nextflow.config b/modules/nf-core/picrust2/pipeline/tests/nextflow.config new file mode 100644 index 00000000000..0bb42a35b9b --- /dev/null +++ b/modules/nf-core/picrust2/pipeline/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: PICRUST2_PIPELINE { + ext.args = "--in_traits 'EC' -t sepp --remove_intermediate" + } +}