Module complementbed added

software/bedtools/complementbed/Dockerfile

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+FROM nfcore/base
+LABEL authors="Jose Espinosa-Carrasco" \
+    description="Docker image containing all requirements for nf-core/modules/bedtools/complementbed"
+
+COPY environment.yml /
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/nf-core-bedtools-complementbed/bin:$PATH

software/bedtools/complementbed/environment.yml

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+# You can use this file to create a conda environment for this pipeline:
+#   conda env create -f environment.yml
+name: nf-core-bedtools-complementbed
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bedtools=2.29.2

software/bedtools/complementbed/main.nf

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+process COMPLEMENT_BED {
+    tag {input_file}
+
+    container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
+
+    input:
+        path (input_file)
+        path (fasta_sizes)
+        val (complementbed_args)
+
+    output:
+        stdout()
+
+    script:
+    """
+    bedtools complement -i ${input_file} -g ${fasta_sizes} ${complementbed_args}
+    """
+}

software/bedtools/complementbed/meta.yml

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+name: bedtools complement
+description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file
+keywords:
+    - complement
+tools:
+    - bedtools:
+        description: |
+            Bedtools is a software package that provides with a toolset to perform genome arithmetic operations.
+        homepage: https://bedtools.readthedocs.io/en/latest/index.html
+        documentation: https://bedtools.readthedocs.io/en/latest/index.html
+        doi: 10.093/bioinformatics/btq033
+input:
+    -
+        - input_file:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bed,gff,vcf}"
+        - fasta_sizes:
+            type: file
+              description: Genome chromosome sizes
+              pattern: "*.{txt,sizes}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,gff,vcf}"
+authors:
+    - "@JoseEspinosa"

software/bedtools/complementbed/test/input_data/A.bed

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+chr1	951	1061
+chr1	1300	1420
+chr1	1400	1500
+
+

software/bedtools/complementbed/test/input_data/genome.sizes

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+chr1	1780869

software/bedtools/complementbed/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.complementbed_args = ''
+
+include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
+include COMPLEMENT_BED from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('./input_data/A.bed')
+chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
+
+// Run the workflow
+workflow {
+    COMPLEMENT_BED(ch_input, chrom_sizes, params.complementbed_args)
+    // .check_output()
+}

software/bedtools/complementbed/test/nextflow.config

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+docker.enabled = true
+params.outdir = './results'