nf-core
diff --git a/‎modules/nf-core/t1k/run/environment.yml‎
Lines changed: 7 additions & 0 deletions b/‎modules/nf-core/t1k/run/environment.yml‎
Lines changed: 7 additions & 0 deletions
diff --git a/‎modules/nf-core/t1k/run/main.nf‎
Lines changed: 84 additions & 0 deletions b/‎modules/nf-core/t1k/run/main.nf‎
Lines changed: 84 additions & 0 deletions
diff --git a/‎modules/nf-core/t1k/run/meta.yml‎
Lines changed: 193 additions & 0 deletions b/‎modules/nf-core/t1k/run/meta.yml‎
Lines changed: 193 additions & 0 deletions
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::t1k=1.0.9"
@@ -0,0 +1,84 @@
+process T1K_RUN {
+    tag "${meta.id}"
+    label 'process_low'
+
+    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/c6/c64676623c43855d3a9dd8a5b02a03b13216e454a8bd1e9a7d9d5695daf5030b/data'
+        : 'community.wave.seqera.io/library/t1k:1.0.9--793c68c25d680b97'}"
+
+    input:
+    tuple val(meta), path(input), path(fasta), path(cordinates), path(barcodes), path(barcodewhitelist)
+
+    output:
+    tuple val(meta), path("*_genotype.tsv")       , emit: genotype_tsv
+    tuple val(meta), path("*_allele.tsv")         , emit: allele_tsv
+    tuple val(meta), path("*_allele.vcf")         , emit: allele_vcf
+    tuple val(meta), path("*_candidate*.fq")      , optional: true, emit: candidate_reads
+    tuple val(meta), path("*_aligned.fa")         , optional: true, emit: aligned_reads_single
+    tuple val(meta), path("*_aligned_{1,2}.fa")   , optional: true, emit: aligned_reads_paired
+    tuple val(meta), path("*_barcode_expr.tsv")   , optional: true, emit: barcode_tsv
+    tuple val(meta), path("*_candidate_bc.fa")    , optional: true, emit: barcode_candidate
+    tuple val(meta), path("*_aligned_bc.fa")      , optional: true, emit: barcode_aligned
+    tuple val("${task.process}"), val('t1k'), eval("run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2"), topic: versions, emit: versions_t1k
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_bam = input.toString().endsWith('.bam')
+    def input_args = ""
+    if (is_bam) {
+        // BAM input
+        input_args = "-b ${input}"
+    }
+    else if (meta.single_end) {
+        // Single-end FASTQ
+        input_args = "-u ${input}"
+    }
+    else if (!meta.single_end && input.size() == 2) {
+        // Paired-end FASTQ
+        input_args = "-1 ${input[0]} -2 ${input[1]}"
+    }
+    else if (!meta.single_end && input.size() == 1) {
+        // Interleaved FASTQ
+        input_args = "-i ${input}"
+    }
+    else {
+        error "Invalid input files for sample ${meta.id}. Please provide either a BAM file, single-end FASTQ, paired-end FASTQ (2 files), or interleaved FASTQ."
+    }
+    def cordinates_args = cordinates && is_bam ? "-c ${cordinates}" : ''
+    def barcodes_args = barcodes ? "--barcode ${barcodes}" : ''
+    def barcodewhitelist_args = barcodewhitelist ? "--barcodeWhiteList ${barcodewhitelist} " : ''
+    """
+    run-t1k \\
+        ${args} \\
+        -t ${task.cpus} \\
+        -o ${prefix} \\
+        -f ${fasta} \\
+        ${input_args} \\
+        ${cordinates_args} \\
+        ${barcodes_args} \\
+        ${barcodewhitelist_args}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+
+    touch ${prefix}_genotype.tsv
+    touch ${prefix}_allele.tsv
+    touch ${prefix}_candidate_1.fq
+    touch ${prefix}_candidate_2.fq
+    touch ${prefix}_aligned_1.fa
+    touch ${prefix}_aligned_2.fa
+    touch ${prefix}_allele.vcf
+    touch ${prefix}_barcode_expr.tsv
+    touch ${prefix}_aligned_bc.fa
+    touch ${prefix}_candidate_bc.fa
+    """
+}
@@ -0,0 +1,193 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "t1k_run"
+description: write your description here
+keywords:
+  - polymorphic
+  - genes
+  - HLA
+  - Kir
+tools:
+  - "t1k":
+      description: "T1K is a versatile methods to genotype highly polymorphic genes
+        (e.g. KIR, HLA) with RNA-seq, WGS or WES data."
+      homepage: "https://github.com/mourisl/T1K/blob/v1.0.8/README.md"
+      documentation: "https://github.com/mourisl/T1K/blob/v1.0.8/README.md"
+      tool_dev_url: "https://github.com/mourisl/T1K"
+      doi: "10.1101/gr.277585.122"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample id and single_end label for fastq input files.
+          e.g. `[ id:'sample1', single_end:false ]`
+    - input:
+        type: file
+        description: BAM or FASTQ file(s).
+        pattern: "*.{bam,fastq}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572 # BAM
+          - edam: http://edamontology.org/format_1930 # FASTQ
+    - fasta:
+        type: file
+        description: Reference fasta file.
+        pattern: "*.{fa,fasta}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+    - cordinates:
+        type: file
+        description: A fasta file with the coordinates of the gene alleles in the
+          header as created form the t1k/build
+        pattern: "*.fa"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
+    - barcodes:
+        type: file
+        description: A file with a list of barcodes.
+        pattern: "*.txt"
+        ontologies:
+          - edam: http://edamontology.org/format_2330
+    - barcodewhitelist:
+        type: file
+        description: A file with a whitelist of barcodes.
+        pattern: "*.txt"
+        ontologies:
+          - edam: http://edamontology.org/format_2330 # TXT
+
+output:
+  genotype_tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_genotype.tsv":
+          type: file
+          description: Genotyping file where the allele for each gene has its own
+            line.
+          pattern: "*_genotype.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 #TSV
+  allele_tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_allele.tsv":
+          type: file
+          description: File with the representative alleles and their quality
+            scores.
+          pattern: "*_allele.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  allele_vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_allele.vcf":
+          type: file
+          description: A vcf file with the novel SNPs.
+          ontologies:
+            - edam: http://edamontology.org/format_3016 # VCF
+  candidate_reads:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_candidate*.fq":
+          type: file
+          description: Fastq file containing candidate reads extracted from raw
+            data for genotyping.
+          ontologies:
+            - edam: http://edamontology.org/format_1930 # FASTQ
+  aligned_reads_single:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_aligned.fa":
+          type: file
+          description: Aligned reads in fasta format from single-end input.
+          pattern: "*_aligned.fa"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  aligned_reads_paired:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_aligned_{1,2}.fa":
+          type: file
+          description: Aligned reads in fasta format from paired-end input.
+          pattern: "*_aligned_{1,2}.fa"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  barcode_tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_barcode_expr.tsv":
+          type: file
+          description: Data matrix where rows are the barcodes and columns are the
+            allele abundances.
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  barcode_candidate:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_candidate_bc.fa":
+          type: file
+          description: Barcodes form candidate reads.
+          pattern: "*_candidate_bc.fa"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  barcode_aligned:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*_aligned_bc.fa":
+          type: file
+          description: Barcodes form aligned reads.
+          pattern: "*_aligned_bc.fa"
+          ontologies:
+            - edam: http://edamontology.org/format_1929 # FASTA
+  versions_t1k:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - t1k:
+          type: string
+          description: The name of the tool
+      - run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - t1k:
+          type: string
+          description: The name of the tool
+      - run-t1k 2>&1 | head -n 1 | cut -d '-' -f 1 | cut -d v -f 2:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@georgiakes"
+maintainers:
+  - "@georgiakes"