add module telseq (#6678)

* add module telseq

* lint code

* fix quote in meta

* fix lint

* fix_indent

* fix_indent

* fix_indent

* fix_indent

* fix_indent

* fix_indent

* add bed test

* fix snap

modules/nf-core/telseq/environment.yml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::telseq=0.0.2

modules/nf-core/telseq/main.nf

@@ -0,0 +1,62 @@
+process TELSEQ {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5ce2a0c04652b0d0cc87f012a2240e1e5a90bc90:eb084e8aa92146f3987d00af8d38b36214d1f39f-0':
+        'biocontainers/mulled-v2-5ce2a0c04652b0d0cc87f012a2240e1e5a90bc90:eb084e8aa92146f3987d00af8d38b36214d1f39f-0' }"
+
+    input:
+    tuple val(meta ), path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(bed)
+
+    output:
+    tuple val(meta), path("*.telseq.tsv"), emit: output
+    path "versions.yml"                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def exome  = bed ? " --exomebed=${bed}" : ""
+    """
+    # telseq doesn't support CRAM. See https://github.com/zd1/telseq/issues/26
+    if ${bam.name.endsWith(".cram")}
+    then
+        samtools view -T ${fasta} -O BAM --uncompressed ${bam} |\\
+        telseq ${args} ${exome} - > tmp.tsv
+    else
+        telseq ${args} ${exome} ${bam} > tmp.tsv
+    fi
+
+    #
+    # 'bug' in telseq, messages that should be printed on stderr are printed on stdout
+    # We remove them with awk
+    #
+    awk '/^ReadGroup/ {ok=1;} {if(ok) print;}' tmp.tsv > ${prefix}.telseq.tsv
+    rm tmp.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        telseq: \$(telseq --help 2>&1 | grep "^Version" -m1 | cut -d ' ' -f2)
+        samtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.telseq.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        telseq: \$(telseq --help 2>&1 | grep "^Version" -m1 | cut -d ' ' -f2)
+        samtools: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}

modules/nf-core/telseq/meta.yml

@@ -0,0 +1,89 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "telseq"
+description: "Telseq: a software for calculating telomere length"
+keywords:
+  - bam
+  - cram
+  - genomics
+  - samtools
+  - telomere
+  - telseq
+tools:
+  - "telseq":
+      description: "A software for calculating telomere length"
+      homepage: "https://github.com/zd1/telseq"
+      documentation: "https://github.com/zd1/telseq"
+      tool_dev_url: "https://github.com/zd1/telseq"
+      doi: "10.1093/nar/gku181"
+      licence: ["GPL v3"]
+      args_id: "$args"
+      identifier: ""
+  - samtools:
+      description: Tools for dealing with SAM, BAM and CRAM files
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/samtools.html
+      tool_dev_url: https://github.com/samtools/samtools
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+      identifier: "biotools:samtools"
+input:
+  - - "meta ":
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'genome' ]
+    - bam:
+        type: file
+        description: BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+    - bai:
+        type: file
+        description: bam index file
+        pattern: "*.{bai,crai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference genome file
+        pattern: "*.{fa,fasta}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference index information
+          e.g. [ id:'genome' ]
+    - fai:
+        type: file
+        description: Fasta index file
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing bed information
+          e.g. [ id:'genome' ]
+    - bed:
+        type: file
+        description: Optional exome regions in BED format. These regions will be excluded
+        pattern: "*.bed"
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.telseq.tsv":
+          type: file
+          description: Telseq output
+          pattern: "*.tsv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@lindenb"
+maintainers:
+  - "@lindenb"

modules/nf-core/telseq/tests/main.nf.test

@@ -0,0 +1,122 @@
+// nf-core modules test telseq
+nextflow_process {
+
+    name "Test Process TELSEQ"
+    script "../main.nf"
+    process "TELSEQ"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "telseq"
+
+    test("sarscov2 - cram") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'cram' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ]
+                input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[3] = [ [] , [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                   process.out.output[0][1],
+                   process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'bam' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[3] = [ [] , [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                   process.out.output[0][1],
+                   process.out.versions).match() }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - bed") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'bambed' ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[3] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                   process.out.output[0][1],
+                   process.out.versions).match() }
+            )
+        }
+    }
+
+
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'stub', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
+                input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                input[3] = [ [] , [] ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                   process.out.output[0][1],
+                   process.out.versions).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/telseq/tests/main.nf.test.snap

@@ -0,0 +1,54 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+             "stub.telseq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+             [
+                 "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610"
+             ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T14:09:45.936712383"
+    },
+    "sarscov2 - cram": {
+        "content": [
+             "cram.telseq.tsv:md5,82005b49e17f114e8ad759dd9d520912",
+             [
+                 "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610"
+             ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T14:09:09.775504172"
+    },
+    "sarscov2 - bam": {
+        "content": [
+             "bam.telseq.tsv:md5,82005b49e17f114e8ad759dd9d520912",
+             [
+                 "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610"
+             ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T14:09:27.747371336"
+    },
+    "sarscov2 - bam - bed": {
+        "content": [
+             "bambed.telseq.tsv:md5,58374f99d395fa64ea561aca73fd6c89",
+             [
+                 "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610"
+             ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-20T14:09:27.747371336"
+    }
+}

modules/nf-core/telseq/tests/tags.yml

@@ -0,0 +1,2 @@
+telseq:
+  - "modules/nf-core/telseq/**"