Merge branch 'dsl2' into quarto

bin/create_acc2tax.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+import argparse
+import pysam
+from pathlib import Path
+
+
+def parse_args():
+    parser = argparse.ArgumentParser("Create acc2tax file")
+    parser.add_argument("genome", type=Path, help="Path to genome file")
+    parser.add_argument("-t", type=int, dest="taxid", help="taxid")
+
+    return parser.parse_args()
+
+
+def acc2tax(genome, taxid):
+    entry_dict = dict()
+    with pysam.FastxFile(genome) as fh:
+        for entry in fh:
+            entry_dict[entry.name] = [entry.name.split(".")[0], taxid]
+    with open(f"{taxid}.accession2taxid", "w") as fh:
+        fh.write("accession\taccession.version\ttaxid\n")
+        for k, v in entry_dict.items():
+            fh.write(f"{v[0]}\t{k}\t{v[1]}\n")
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    acc2tax(args.genome, args.taxid)

bin/sam2lca_json.py

@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+
+
+import os
+import json
+import argparse
+from pathlib import Path
+
+
+def parse_args():
+    parser = argparse.ArgumentParser("Create sam2lca json file")
+    parser.add_argument(
+        "acc2taxid", type=Path, help="Path to accession2taxid gzip compressed file"
+    )
+    parser.add_argument(
+        "md5",
+        type=Path,
+        help="Path to accession2taxid gzip compressed md5 checksum file",
+    )
+
+    return parser.parse_args()
+
+
+def write_json(acc2taxid, md5, db_name="adnamap"):
+    sam2lca_dict = {
+        "mapfiles": {db_name: [acc2taxid.as_posix()]},
+        "mapmd5": {db_name: [md5.as_posix()]},
+        "map_db": {db_name: f"{db_name}.db"},
+    }
+    with open(f"{db_name}.sam2lca.json", "w") as fh:
+        json.dump(sam2lca_dict, fh)
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    write_json(args.acc2taxid, args.md5)

modules/local/create_acc2tax.nf

@@ -0,0 +1,22 @@
+process CREATE_ACC2TAX {
+    tag "${meta.genome_name}"
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::sam2lca=1.1.4" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sam2lca:1.1.4--pyhdfd78af_0' :
+        'quay.io/biocontainers/sam2lca:1.1.4--pyhdfd78af_0'            }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    path("*.accession2taxid"), emit: acc2tax
+
+    script:
+    def args = task.ext.args ?: ""
+
+    """
+    create_acc2tax.py $fasta -t ${meta.taxid}
+    """
+}

modules/local/sam2lca/prep_db/main.nf

@@ -0,0 +1,25 @@
+process SAM2LCA_PREPDB {
+    label 'process_single'
+
+    conda (params.enable_conda ? "bioconda::sam2lca=1.1.4--pyhdfd78af_0" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sam2lca:1.1.4--pyhdfd78af_0' :
+        'quay.io/biocontainers/sam2lca:1.1.4--pyhdfd78af_0'            }"
+
+    input:
+    path(acc2tax)
+
+    output:
+    path("*.md5"), emit: acc2tax_md5
+    path("*.json"), emit: acc2tax_json
+    path("*.gz"), emit: acc2tax_gz
+
+    script:
+    def args = task.ext.args ?: ""
+
+    """
+    gzip $acc2tax
+    md5sum ${acc2tax}.gz > ${acc2tax}.gz.md5
+    sam2lca_json.py ${acc2tax}.gz ${acc2tax}.gz.md5
+    """
+}

modules/local/sam2lca/updatedb/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::sam2lca=1.1.4"

modules/local/sam2lca/updatedb/main.nf

@@ -0,0 +1,62 @@
+process SAM2LCA_UPDATEDB {
+    tag "${acc2tax_name}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sam2lca:1.1.4--pyhdfd78af_0':
+        'biocontainers/sam2lca:1.1.4--pyhdfd78af_0' }"
+
+    input:
+        val(acc2tax_name)
+        val(taxo_db_name)
+        path(taxo_nodes)// nodes.dmp
+        path(taxo_names) // names.dmp
+        path(taxo_merged) // merged.dmp
+        path(acc2tax_json) // optional
+        path(acc2tax) // acc2tax.gz
+        path(acc2tax_md5) // acc2tax.gz.md5
+
+    output:
+        path "sam2lca_db" , emit: sam2lca_db
+        path "versions.yml" , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def names = taxo_names ? "--taxo_names ${taxo_names}" : ''
+        def nodes = taxo_nodes ? "--taxo_nodes ${taxo_nodes}" : ''
+        def merged = taxo_merged ? "--taxo_merged ${taxo_merged}" : ''
+        def json = acc2tax_json ? "--acc2tax_json ${acc2tax_json}" : ''
+        """
+        mkdir -p sam2lca_db
+
+        sam2lca -d sam2lca_db \\
+            update-db \\
+            -t $taxo_db_name \\
+            $names \\
+            $nodes \\
+            $merged \\
+            -a $acc2tax_name \\
+            $json \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            sam2lca: \$(echo \$(sam2lca --version 2>&1) | sed 's/^sam2lca, version //' )
+        END_VERSIONS
+        """
+
+    stub:
+        """
+        mkdir -p sam2lca_db
+        touch sam2lca_db/test.pkl
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            sam2lca: \$(echo \$(sam2lca --version 2>&1) | sed 's/^sam2lca, version //' )
+        END_VERSIONS
+        """
+}

modules/local/sam2lca/updatedb/meta.yml

@@ -0,0 +1,80 @@
+name: "sam2lca_updatedb"
+description: Build sam2lca database for calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM
+  files
+keywords:
+  - LCA
+  - alignment
+  - bam
+  - metagenomics
+  - Ancestor
+  - multimapper
+  - build
+  - database
+tools:
+  - "sam2lca":
+      description: "Lowest Common Ancestor on SAM/BAM/CRAM alignment files"
+      homepage: "https://github.com/maxibor/sam2lca"
+      documentation: "https://sam2lca.readthedocs.io"
+      doi: "10.21105/joss.04360"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  -  - acc2tax_name:
+        type: string
+        description: Name of accession2taxid type to use
+  -  - taxo_db_name:
+        type: string
+        description: Name of taxonomy dabase type to use
+  -  - taxo_nodes:
+        type: file
+        description: "NCBI taxonomy nodes file"
+        pattern: "*.dmp"
+        ontologies:
+          - edam: http://edamontology.org/format_2330
+  -  - taxo_names:
+        type: file
+        description: NCBI taxonomy names file
+        pattern: "*.dmp"
+        ontologies:
+          - edam: http://edamontology.org/format_2330
+  -  - taxo_merged:
+        type: file
+        description: NCBI taxonomy merged file
+        pattern: "*.dmp"
+        ontologies:
+          - edam: http://edamontology.org/format_2330
+  -  - acc2tax_json:
+        type: file
+        description: JSON file listing accession2taxid mapping files. Only required if using a custom database
+        pattern: "*.json"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464"
+  -  - acc2tax:
+        type: string
+        description: accession2taxid mapping file compressed with gzip. Only required if using a custom database
+        pattern: "*.gz"
+        ontologies:
+          - edam: http://edamontology.org/format_3989
+  -  - acc2tax_md5:
+        type: file
+        description: MD5 checksum of the accession2taxid mapping file. Only required if using a custom database
+        pattern: "*.md5"
+        ontologies:
+          - edam: http://edamontology.org/format_2330
+
+output:
+  - sam2lca_db:
+    - sam2lca_db:
+        type: directory
+        description: "sam2lca database"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@maxibor"
+maintainers:
+  - "@maxibor"

modules/local/sam2lca/updatedb/tests/main.nf.test

@@ -0,0 +1,35 @@
+nextflow_process {
+
+    name "Test Process SAM2LCA_UPDATEDB"
+    script "../main.nf"
+    process "SAM2LCA_UPDATEDB"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sam2lca"
+    tag "sam2lca/updatedb"
+
+    test("test-sam2lca-updatedb - test dataset") {
+        when {
+            process {
+                """
+                input[0] = 'test'
+                input[1] = 'test'
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                input[6] = []
+                input[7] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+
+}

modules/local/sam2lca/updatedb/tests/main.nf.test.snap

@@ -0,0 +1,92 @@
+{
+    "test-sam2lca-updatedb - test taxonomy": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "merged.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "merged.dmp.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "merged.dmp.gz.md5:md5,f6e01130c21a58a3371eddec53a18f6f",
+                        "names.dmp:md5,e7994ec89470481e031b3ecef616e778",
+                        "names.dmp.gz:md5,e7994ec89470481e031b3ecef616e778",
+                        "names.dmp.gz.md5:md5,ce7546bbac7dcbe5c0054975538d7fb7",
+                        "nodes.dmp:md5,9e934f98f3c2ace17fa3d77eb235f96f",
+                        "nodes.dmp.gz:md5,9e934f98f3c2ace17fa3d77eb235f96f",
+                        "nodes.dmp.gz.md5:md5,a4597c31842067abe62dda359f8bd854",
+                        [
+                            "000005.log:md5,9167e183e1dc6070dbfc81c4674d9654",
+                            "CURRENT:md5,6752a1d65b201c13b62ea44016eb221f",
+                            "IDENTITY:md5,730568fb30c4bd8dc6db1b95d288b9dc",
+                            "LOCK:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "LOG:md5,a6e02bcd897ccd9a28a40cf3dd350292",
+                            "MANIFEST-000004:md5,17211b4c15bffd11c80dfbd5b7db77ef",
+                            "OPTIONS-000007:md5,22187b853e27d095e1eac121574b1d95"
+                        ],
+                        "test.pkl:md5,d9f5e1d08d7b678281ac088cdca355c9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,175fb2cc18a30f7ab660efe1a42b7161"
+                ],
+                "sam2lca_db": [
+                    [
+                        "merged.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "merged.dmp.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "merged.dmp.gz.md5:md5,f6e01130c21a58a3371eddec53a18f6f",
+                        "names.dmp:md5,e7994ec89470481e031b3ecef616e778",
+                        "names.dmp.gz:md5,e7994ec89470481e031b3ecef616e778",
+                        "names.dmp.gz.md5:md5,ce7546bbac7dcbe5c0054975538d7fb7",
+                        "nodes.dmp:md5,9e934f98f3c2ace17fa3d77eb235f96f",
+                        "nodes.dmp.gz:md5,9e934f98f3c2ace17fa3d77eb235f96f",
+                        "nodes.dmp.gz.md5:md5,a4597c31842067abe62dda359f8bd854",
+                        [
+                            "000005.log:md5,9167e183e1dc6070dbfc81c4674d9654",
+                            "CURRENT:md5,6752a1d65b201c13b62ea44016eb221f",
+                            "IDENTITY:md5,730568fb30c4bd8dc6db1b95d288b9dc",
+                            "LOCK:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "LOG:md5,a6e02bcd897ccd9a28a40cf3dd350292",
+                            "MANIFEST-000004:md5,17211b4c15bffd11c80dfbd5b7db77ef",
+                            "OPTIONS-000007:md5,22187b853e27d095e1eac121574b1d95"
+                        ],
+                        "test.pkl:md5,d9f5e1d08d7b678281ac088cdca355c9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,175fb2cc18a30f7ab660efe1a42b7161"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T14:42:14.067314457"
+    },
+    "sam2lca-updatedb - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "test.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,175fb2cc18a30f7ab660efe1a42b7161"
+                ],
+                "sam2lca_db": [
+                    [
+                        "test.pkl:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,175fb2cc18a30f7ab660efe1a42b7161"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-22T14:43:21.32148453"
+    }
+}