Module bedtools-merge added

software/bedtools/merge/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-merge/bin:$PATH

software/bedtools/merge/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-merge
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bedtools=2.29.2

software/bedtools/merge/main.nf

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+process BEDTOOLS_MERGE {
+    tag { input_file }
+
+    container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
+
+    input:
+    path (input_file)
+    val (bedtools_merge_args)
+
+    output:
+    stdout()
+
+    script:
+    """
+    bedtools merge -i ${input_file} ${bedtools_merge_args}
+    """
+}

software/bedtools/merge/meta.yml

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+name: bedtools merge
+description: Combines overlapping genome features of a single file
+keywords:
+    - merge
+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,bam}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed}"
+authors:
+    - "@JoseEspinosa"

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

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

software/bedtools/merge/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.bedtools_merge_args = '' //''-s -c 6 -o distinct'
+
+include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
+include BEDTOOLS_MERGE from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('../../test_data_set/A.bed')
+//ch_input = Channel.fromPath('./input_data/JK2067_downsampled_s0.1.bam')
+
+// Run the workflow
+workflow {
+    BEDTOOLS_MERGE(ch_input, params.bedtools_merge_args)
+    // .check_output()
+}

software/bedtools/merge/test/nextflow.config

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