Merge pull request #42 from JoseEspinosa/bedtools_dev

Add modules complement, genomecov, intersect, merge, sort for bedtools

software/bedtools/complement/Dockerfile

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

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

software/bedtools/complement/main.nf

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+def MODULE = "bedtools_complement"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
+process BEDTOOLS_COMPLEMENT {
+    tag {input_file}
+
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    container "docker.pkg.github.com/nf-core/$MODULE"
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    path (input_file)
+    path (fasta_sizes)
+    val (bedtools_complement_args)
+
+    output:
+    path "${input_file}.bed", emit: complement
+    path "*.version.txt", emit: version
+
+    script:
+    """
+    bedtools complement -i ${input_file} -g ${fasta_sizes} ${bedtools_complement_args} > ${input_file}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
+    """
+}

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

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+../../../../../tests/data/bed/A.bed

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

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+../../../../../tests/data/bed/genome.sizes

software/bedtools/complement/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
+params.bedtools_complement_args = ''
+
+include BEDTOOLS_COMPLEMENT 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 {
+    BEDTOOLS_COMPLEMENT(ch_input, chrom_sizes, params.bedtools_complement_args)
+}

software/bedtools/genomecov/Dockerfile

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

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

software/bedtools/genomecov/main.nf

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+def MODULE = "bedtools_genomecov"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
+process BEDTOOLS_GENOMECOV {
+    tag {bam}
+
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    container "docker.pkg.github.com/nf-core/$MODULE"
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    path (bam)
+    path (chrom_sizes)
+    val (bedtools_genomecov_args)
+
+    output:
+    path "${bam}.bed", emit: coverage
+    path "*.version.txt", emit: version
+
+    script:
+    """
+    bedtools genomecov -ibam ${bam} -g ${chrom_sizes} ${bedtools_genomecov_args} > ${bam}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
+    """
+}

software/bedtools/genomecov/meta.yml

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+name: bedtools genomecov
+description: Returns feature coverage for a given genome in different formats
+keywords:
+    - genomecov
+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: "*.{bam}"
+        - chrom_sizes:
+            type: file
+            description: Genome chromosome sizes
+            pattern: "*.{txt,sizes}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,bedGraph}"
+authors:
+    - "@JoseEspinosa"

software/bedtools/genomecov/test/input_data/JK2067_downsampled_s0.1.bam

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+../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

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

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+../../../../../tests/data/bed/genome.sizes

software/bedtools/genomecov/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
+params.bedtools_genomecov_args = '' //'-bg'
+
+include BEDTOOLS_GENOMECOV from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('./input_data/JK2067_downsampled_s0.1.bam')
+chrom_sizes = Channel.fromPath('./input_data/genome.sizes')
+
+// Run the workflow
+workflow {
+    BEDTOOLS_GENOMECOV(ch_input, chrom_sizes, params.bedtools_genomecov_args)
+}

software/bedtools/intersect/Dockerfile

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

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

software/bedtools/intersect/main.nf

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+def MODULE = "bedtools_intersect"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
+process INTERSECT_BED {
+    tag "$input_file_1-$input_file_2"
+
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    container "docker.pkg.github.com/nf-core/$MODULE"
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    path (input_file_1)
+    path (input_file_2)
+    val (intersectbed_args)
+
+    output:
+    path "${input_file_1.baseName}_i_${input_file_2.baseName}.bed", emit: intersect
+    path "*.version.txt", emit: version
+
+    script:
+    def params_string = intersectbed_args.collect {
+                            /-$it.key $it.value/
+                        } join " "
+
+    """
+    bedtools intersect -a ${input_file_1} -b ${input_file_2} ${params_string} > ${input_file_1.baseName}_i_${input_file_2.baseName}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
+    """
+}
+

software/bedtools/intersect/meta.yml

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+name: bedtools intersect
+description: Returns the overlapping features between two sets of genomics features
+keywords:
+    - bedtools intersect
+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_1:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bam,bed,BED,gff,vcf}"
+        - input_file_2:
+            type: file
+            description: Input genomic coordinates file
+            pattern: "*.{bam,bed,BED,gff,vcf}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,BED}"
+authors:
+    - "@JoseEspinosa"

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

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+../../../../../tests/data/bed/A.bed

software/bedtools/intersect/test/input_data/B.bed

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+../../../../../tests/data/bed/B.bed

software/bedtools/intersect/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
+params.intersect_args = '' //'-bed -c -f 0.20'
+
+include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
+include INTERSECT_BED from '../main.nf' params(params)
+
+// Define input channels
+ch_input_1 = Channel.fromPath('./input_data/A.bed')
+ch_input_2 = Channel.fromPath('./input_data/B.bed')
+
+def additional_params_map = [:]
+
+additional_params_map =  [ s: "",
+                           f: 0.9 ]
+
+// Run the workflow
+workflow {
+    INTERSECT_BED(ch_input_1, ch_input_2, additional_params_map)
+}

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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+def MODULE = "bedtools_merge"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
+process BEDTOOLS_MERGE {
+    tag { input_file }
+
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    container "docker.pkg.github.com/nf-core/$MODULE"
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    path (input_file)
+    val (bedtools_merge_args)
+
+    output:
+    path "${input_file}.bed", emit: merge
+    path "*.version.txt", emit: version
+
+    script:
+    """
+    bedtools merge -i ${input_file} ${bedtools_merge_args} > ${input_file}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
+    """
+}

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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+../../../../../tests/data/bed/A.bed

software/bedtools/merge/test/input_data/JK2067_downsampled_s0.1.bam

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+../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

software/bedtools/merge/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
+params.bedtools_merge_args = '' //''-s -c 6 -o distinct'
+
+include BEDTOOLS_MERGE from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('./input_data/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)
+}

software/bedtools/merge/test/nextflow.config

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

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

software/bedtools/sort/main.nf

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+def MODULE = "bedtools_sort"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
+process BEDTOOLS_SORT {
+    tag { input_file }
+
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    container "docker.pkg.github.com/nf-core/$MODULE"
+
+    conda "${moduleDir}/environment.yml"
+
+    input:
+    path (input_file)
+    val (bedtools_sort_args)
+
+    output:
+    path "${input_file}.bed", emit: sort
+    path "*.version.txt", emit: version
+
+    script:
+    """
+    bedtools sort -i ${input_file} ${bedtools_sort_args} > ${input_file}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
+    """
+}

software/bedtools/sort/meta.yml

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+name: bedtools sort
+description: Returns a sorted feature file by chromosome and other criteria
+keywords:
+    - sort
+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}"
+
+output:
+    -
+        - index:
+            type: stdout,file
+            description:
+            pattern: "stdout,*.{bed,gff,vcf}"
+authors:
+    - "@JoseEspinosa"

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

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+../../../../../tests/data/bed/A.bed

software/bedtools/sort/test/main.nf

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+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
+params.bedtools_sort_args = '' //'-sizeD'
+
+include BEDTOOLS_SORT from '../main.nf' params(params)
+
+// Define input channels
+ch_input = Channel.fromPath('./input_data/A.bed')
+
+// Run the workflow
+workflow {
+    BEDTOOLS_SORT(ch_input, params.bedtools_sort_args)
+}

tests/data/bed/A.bed

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

tests/data/bed/B.bed

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+chr1	999	1010

tests/data/bed/genome.sizes

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+chr1	1780869