Merge branch 'master' of https://github.com/nf-core/modules into split_tests

.github/workflows/pytest-workflow.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         nxf_version: ['20.11.0-edge']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
-        profile: ['docker', 'singularity', 'conda']
+        profile: ['docker'] ## 'conda', 'singularity'
     env:
       NXF_ANSI_LOG: false
     steps:
@@ -72,8 +72,11 @@ jobs:
         uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          channels: defaults, bioconda, conda-forge
+          channels: conda-forge,bioconda,defaults
           python-version: ${{ matrix.python-version }}
+      - name: Conda clean
+        if: matrix.profile == 'conda'
+        run: conda clean -a
 
       # Test the module
       - name: Run pytest-workflow

deprecated/bedtools/complement/Dockerfile

@@ -1,7 +0,0 @@
-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

deprecated/bedtools/complement/environment.yml

@@ -1,9 +0,0 @@
-# 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

deprecated/bedtools/complement/main.nf

@@ -1,32 +0,0 @@
-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
-    """
-}

deprecated/bedtools/complement/meta.yml

@@ -1,30 +0,0 @@
-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"

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/A.bed

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/genome.sizes

deprecated/bedtools/complement/test/main.nf

@@ -1,19 +0,0 @@
-#!/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)
-}

deprecated/bedtools/genomecov/Dockerfile

@@ -1,7 +0,0 @@
-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

deprecated/bedtools/genomecov/environment.yml

@@ -1,9 +0,0 @@
-# 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

deprecated/bedtools/genomecov/main.nf

@@ -1,32 +0,0 @@
-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
-    """
-}

deprecated/bedtools/genomecov/meta.yml

@@ -1,30 +0,0 @@
-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"

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

@@ -1 +0,0 @@
-../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/genome.sizes

deprecated/bedtools/genomecov/test/main.nf

@@ -1,19 +0,0 @@
-#!/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)
-}

deprecated/bedtools/intersect/Dockerfile

@@ -1,7 +0,0 @@
-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

deprecated/bedtools/intersect/environment.yml

@@ -1,9 +0,0 @@
-# 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

deprecated/bedtools/intersect/main.nf

@@ -1,36 +0,0 @@
-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
-    """
-}

deprecated/bedtools/intersect/meta.yml

@@ -1,30 +0,0 @@
-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"

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/A.bed

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/B.bed

deprecated/bedtools/intersect/test/main.nf

@@ -1,24 +0,0 @@
-#!/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)
-}

deprecated/bedtools/merge/Dockerfile

@@ -1,7 +0,0 @@
-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

deprecated/bedtools/merge/environment.yml

@@ -1,9 +0,0 @@
-# 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

deprecated/bedtools/merge/main.nf

@@ -1,31 +0,0 @@
-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
-    """
-}

deprecated/bedtools/merge/meta.yml

@@ -1,26 +0,0 @@
-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"

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/A.bed

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

@@ -1 +0,0 @@
-../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

deprecated/bedtools/merge/test/main.nf

@@ -1,19 +0,0 @@
-#!/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)
-}

deprecated/bedtools/merge/test/nextflow.config

@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'

deprecated/bedtools/sort/environment.yml

@@ -1,9 +0,0 @@
-# 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

deprecated/bedtools/sort/main.nf

@@ -1,31 +0,0 @@
-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
-    """
-}

deprecated/bedtools/sort/meta.yml

@@ -1,26 +0,0 @@
-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"

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

@@ -1 +0,0 @@
-../../../../../tests/data/bed/A.bed

deprecated/bedtools/sort/test/main.nf

@@ -1,18 +0,0 @@
-#!/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)
-}

deprecated/bowtie2/main.nf

@@ -1,52 +0,0 @@
-nextflow.preview.dsl=2
-params.genome = ''
-
-process BOWTIE2 {
-    // depending on the genome used one might want/need to adjust the memory settings.
-    // For the E. coli test data this is probably not required
-
-    // label 'bigMem'
-    // label 'multiCore'
-
-    publishDir "$outdir/bowtie2",
-        mode: "copy", overwrite: true
-
-    input:
-        tuple val(name), path(reads)
-        val (outdir)
-        val (bowtie2_args)
-        val (verbose)
-
-    output:
-        path "*bam",  emit: bam
-        path "*stats.txt", emit: stats
-
-    script:
-        if (verbose){
-            println ("[MODULE] BOWTIE2 ARGS: " + bowtie2_args)
-        }
-
-        cores = 4
-
-        readString = ""
-
-        // Options we add are
-        bowtie2_options = bowtie2_args
-        bowtie2_options +=  " --no-unal "  // We don't need unaligned reads in the BAM file
-
-        // single-end / paired-end distinction. Might also be handled via params.single_end
-        if (reads instanceof List) {
-            readString = "-1 " + reads[0] + " -2 " + reads[1]
-        }
-        else {
-            readString = "-U " + reads
-        }
-
-        index = params.genome["bowtie2"]
-        bowtie2_name = name + "_" + params.genome["name"]
-
-        """
-        bowtie2 -x ${index} -p ${cores} ${bowtie2_options} ${readString}  2>${bowtie2_name}_bowtie2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${bowtie2_name}_bowtie2.bam
-        """
-
-}

deprecated/bowtie2/meta.yml

@@ -1,37 +0,0 @@
-name: Bowtie 2
-description: Ultrafast alignment to reference genome
-keywords:
-    - Alignment
-    - Short reads
-    - FM Index
-tools:
-    - fastqc:
-        description: |
-            Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads
-            to long reference sequences. It is particularly good at aligning reads of about
-            50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively
-            long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep
-            its memory footprint small: for the human genome, its memory footprint is typically
-            around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
-        homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
-        documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
-input:
-    -
-        - sample_id:
-            type: string
-            description: Sample identifier
-        - reads:
-            type: file
-            description: Input FastQ file, or pair of files
-output:
-    -
-        - report:
-            type: file
-            description: mapping statistics report
-            pattern: "*bowtie2_stats.txt"
-        - alignment:
-            type: file
-            description: alignment file in BAM format
-            pattern: "*bowtie2.bam"
-authors:
-    - "@FelixKrueger"

deprecated/bowtie2/test/indices/E_coli/NC_010473.fa

@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa

deprecated/bowtie2/test/input/Ecoli_DNA_R1.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

deprecated/bowtie2/test/input/Ecoli_DNA_R2.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

deprecated/bowtie2/test/input/test_R1_val_1.fq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

deprecated/bowtie2/test/input/test_R2_val_2.fq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

deprecated/bowtie2/test/main.nf

@@ -1,31 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl=2
-
-params.outdir = "."
-params.genome = ""
-params.bowtie2_args = ''
-// Bowtie2 arguments should be supplied in the following format to work:
-// --bowtie2_args="--score-min L,0,-0.8"
-
-params.verbose = false
-
-if (params.verbose){
-    println ("[WORKFLOW] BOWTIE2 ARGS: "      + params.bowtie2_args)
-}
-
-// for other genomes this needs to be handled somehow to return all possible genomes
-genomeValues = ["name" : params.genome]
-genomeValues["bowtie2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/bowtie2/E_coli/${params.genome}";
-
-include '../main.nf'   params(genome: genomeValues)
-
-ch_read_files = Channel
-  .fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
-  // .view()  // to check whether the input channel works
-
-workflow {
-
-    main:
-        BOWTIE2(ch_read_files, params.outdir, params.bowtie2_args, params.verbose)
-    
-}

deprecated/bowtie2/test/nextflow.config

@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'

deprecated/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2_stats.txt

@@ -1,15 +0,0 @@
-10000 reads; of these:
-  10000 (100.00%) were paired; of these:
-    893 (8.93%) aligned concordantly 0 times
-    8474 (84.74%) aligned concordantly exactly 1 time
-    633 (6.33%) aligned concordantly >1 times
-    ----
-    893 pairs aligned concordantly 0 times; of these:
-      815 (91.27%) aligned discordantly 1 time
-    ----
-    78 pairs aligned 0 times concordantly or discordantly; of these:
-      156 mates make up the pairs; of these:
-        0 (0.00%) aligned 0 times
-        1 (0.64%) aligned exactly 1 time
-        155 (99.36%) aligned >1 times
-100.00% overall alignment rate

deprecated/bowtie2/test/output/test_GRCm38_bowtie2_stats.txt

@@ -1,15 +0,0 @@
-9979 reads; of these:
-  9979 (100.00%) were paired; of these:
-    3584 (35.92%) aligned concordantly 0 times
-    3705 (37.13%) aligned concordantly exactly 1 time
-    2690 (26.96%) aligned concordantly >1 times
-    ----
-    3584 pairs aligned concordantly 0 times; of these:
-      886 (24.72%) aligned discordantly 1 time
-    ----
-    2698 pairs aligned 0 times concordantly or discordantly; of these:
-      5396 mates make up the pairs; of these:
-        2282 (42.29%) aligned 0 times
-        1467 (27.19%) aligned exactly 1 time
-        1647 (30.52%) aligned >1 times
-88.57% overall alignment rate

deprecated/cutadapt/main.nf

@@ -1,41 +0,0 @@
-process cutadapt {
-    tag "${sample_id}"
-
-    container 'quay.io/biocontainers/cutadapt:1.16--py27_1'
-
-    input:
-    tuple val(sample_id), path(reads)
-
-    output:
-    tuple sample_id, path("trimmed_*.fastq")
-
-    script:
-    forward_fq = "trimmed_1.fastq"
-    reverse_fq = "trimmed_2.fastq"
-
-
-    if (params.single_end) {
-        processing = """
-                    cutadapt \
-                        -j ${task.cpus} \
-                        -q $params.cutadapt_min_quality \
-                        --minimum-length $params.cutadapt_min_length \
-                        --output ${forward_fq} \
-                        ${reads}
-                    """
-    } else {
-        processing = """
-                    cutadapt \
-                        -j ${task.cpus} \
-                        -q $params.cutadapt_min_quality \
-                        --minimum-length $params.cutadapt_min_length \
-                        --pair-filter=any \
-                        --output ${forward_fq} \
-                        --paired-output ${reverse_fq} ${reads}
-                    """
-    }
-
-    version = "cutadapt --version &> v_cutadapt.txt"
-
-    return processing + version
-}

deprecated/cutadapt/meta.yml

@@ -1,36 +0,0 @@
-name: Cutadapt
-description: cutadapt removes adapter sequences from high-throughput sequencing reads
-keywords:
-    - Quality Control
-    - QC
-    - Adapters
-tools:
-    - fastqc:
-        description: |
-            Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence
-            from your high-throughput sequencing reads.
-
-            Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’
-            sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads
-            start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but
-            often you don’t want them to be in your reads.
-        homepage: https://cutadapt.readthedocs.io/en/stable/
-        documentation: https://cutadapt.readthedocs.io/en/stable/
-input:
-    -
-        - sample_id:
-            type: string
-            description: Sample identifier
-        - reads:
-            type: file
-            description: Input FastQ file, or pair of files
-output:
-    -
-        - sample_id:
-            type: string
-            description: Sample identifier
-        - reads:
-            type: file
-            description: trimmed FastQ file, or pair of files
-authors:
-    - "@piotr-faba-ardigen"

deprecated/cutadapt/test/main.nf

@@ -1,20 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../main.nf' params(params)
-
-// Define input channels
-input_fastqs = Channel.fromFilePairs('../../../test-datasets/tools/cutadapt/input/*_{1,2}.fastq' )
-
-if(params.single_end){
-    input_fastqs = Channel.from([
-            ['SRR4238351', '../../../test-datasets/tools/cutadapt/input/SRR4238351_subsamp.fastq.gz'],
-            ['SRR4238355', '../../../test-datasets/tools/cutadapt/input/SRR4238355_subsamp.fastq.gz'],
-            ['SRR4238359', '../../../test-datasets/tools/cutadapt/input/SRR4238359_subsamp.fastq.gz'],
-            ['SRR4238379', '../../../test-datasets/tools/cutadapt/input/SRR4238379_subsamp.fastq.gz']
-        ]).map { row -> [ row[0], [ file(row[1]) ] ] }
-}
-
-// Run the workflow
-workflow {
-    cutadapt(input_fastqs)
-}

deprecated/cutadapt/test/nextflow.config

@@ -1,9 +0,0 @@
-docker.enabled = true
-params.outdir = './results'
-
-params{
-    // Preprocessing options
-    cutadapt_min_length = 40
-    cutadapt_min_quality = 25
-    single_end = false
-}

deprecated/hisat2/main.nf

@@ -1,58 +0,0 @@
-nextflow.preview.dsl=2
-params.genome = ''
-
-process HISAT2 {
-    // depending on the genome used one might want/need to adjust the memory settings.
-    // For the E. coli test data this is probably not required
-    // label 'bigMem'
-    // label 'multiCore'
-
-    publishDir "$outdir/hisat2",
-        mode: "copy", overwrite: true
-
-    input:
-        tuple val(name), path(reads)
-        val outdir
-        val hisat2_args
-        val verbose
-
-    output:
-        path "*bam",       emit: bam
-        path "*stats.txt", emit: stats
-
-    script:
-
-        if (verbose){
-            println ("[MODULE] HISAT2 ARGS: " + hisat2_args)
-        }
-
-        cores = 4
-        readString = ""
-        hisat_options = hisat2_args
-
-        // Options we add are
-        hisat_options = hisat_options + " --no-unal --no-softclip "
-
-        if (reads instanceof List) {
-            readString = "-1 "+reads[0]+" -2 "+reads[1]
-            hisat_options = hisat_options + " --no-mixed --no-discordant"
-        }
-        else {
-            readString = "-U "+reads
-        }
-        index = params.genome["hisat2"]
-
-        splices = ''
-        if (params.genome.containsKey("hisat2_splices")){
-            splices = " --known-splicesite-infile " + params.genome["hisat2_splices"]
-        }
-        else{
-            println ("No key 'hisat2_splices' was supplied. Skipping...")
-        }
-        hisat_name = name + "_" + params.genome["name"]
-
-        """
-        hisat2 -p ${cores} ${hisat_options} -x ${index} ${splices} ${readString}  2>${hisat_name}_hisat2_stats.txt | samtools view -bS -F 4 -F 8 -F 256 -> ${hisat_name}_hisat2.bam
-        """
-
-}

deprecated/hisat2/meta.yml

@@ -1,37 +0,0 @@
-name: HISAT2
-description: Graph-based alignment of next generation sequencing reads to a population of genomes
-keywords:
-    - Alignment
-    - Short reads
-    - graph FM Index (GFM)
-    - RNA-seq
-tools:
-    - fastqc:
-        description: |
-            HISAT2 is a fast and sensitive alignment program for mapping next-generation
-            sequencing reads (whole-genome, transcriptome, and exome sequencing data)
-            against the general human population (as well as against a single reference genome).
-            Based on GCSA (an extension of BWT for a graph) it is designed and implemented as a
-            graph FM index (GFM).
-        homepage: http://daehwankimlab.github.io/hisat2/
-        documentation: https://ccb.jhu.edu/software/hisat2/manual.shtml
-input:
-    -
-        - sample_id:
-            type: string
-            description: Sample identifier
-        - reads:
-            type: file
-            description: Input FastQ file, or pair of files
-output:
-    -
-        - report:
-            type: file
-            description: mapping statistics report
-            pattern: "*hisat2_stats.txt"
-        - alignment:
-            type: file
-            description: alignment file in BAM format
-            pattern: "*hisat2.bam"
-authors:
-    - "@FelixKrueger"

deprecated/hisat2/test/indices/E_coli/NC_010473.fa

@@ -1 +0,0 @@
-../../../../../tests/data/fasta/E_coli/NC_010473.fa

deprecated/hisat2/test/input/Ecoli_DNA_R1.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

deprecated/hisat2/test/input/Ecoli_DNA_R2.fastq.gz

@@ -1 +0,0 @@
-../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

deprecated/hisat2/test/main.nf

@@ -1,34 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl=2
-
-params.outdir = "."
-params.genome = ""
-params.hisat2_args = ''
-// HISAT2 arguments should be supplied in the following format to work:
-// --hisat2_args="--score-min L,0,-0.8"
-
-params.verbose = false
-
-if (params.verbose){
-    println ("[WORKFLOW] HISAT2 ARGS ARE: "       + params.hisat2_args)
-}
-// for other genomes this needs to be handled somehow to return all possible genomes
-genomeValues = ["name" : params.genome]
-genomeValues["hisat2"] = "/bi/home/fkrueger/VersionControl/nf-core-modules/test-datasets/indices/hisat2/E_coli/${params.genome}";
-
-include '../main.nf'   params(genome: genomeValues)
-
-ch_read_files = Channel
-  .fromFilePairs('../../../test-datasets/Ecoli*{1,2}.fastq.gz',size:-1)
-  // .view()  // to check whether the input channel works
-
-workflow {
-
-    main:
-        HISAT2(ch_read_files, params.outdir, params.hisat2_args, params.verbose)
-}
-
-
-
-
-

deprecated/hisat2/test/nextflow.config

@@ -1,2 +0,0 @@
-// docker.enabled = true
-params.outdir = './results'

deprecated/hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

@@ -1,6 +0,0 @@
-10000 reads; of these:
-  10000 (100.00%) were paired; of these:
-    823 (8.23%) aligned concordantly 0 times
-    8583 (85.83%) aligned concordantly exactly 1 time
-    594 (5.94%) aligned concordantly >1 times
-91.77% overall alignment rate

deprecated/multiqc/main.nf

@@ -1,31 +0,0 @@
-nextflow.preview.dsl=2
-
-process MULTIQC {
-
-    // tag "FastQC - $sample_id"
-
-    publishDir "${outdir}/multiqc",
-        mode: "copy", overwrite: true
-
-    input:
-        path file
-        val outdir
-        val multiqc_args
-        // multiqc_args are best passed into the workflow in the following manner:
-        // --multiqc_args="--exlude STAR --title custom_report_title"
-        val verbose
-
-    output:
-        path "*html",       emit: html
-
-    script:
-
-        if (verbose){
-            println ("[MODULE] MULTIQC ARGS: " + multiqc_args)
-        }
-
-        """
-        multiqc $multiqc_args -x work .
-        """
-
-}

deprecated/multiqc/meta.yml

@@ -1,26 +0,0 @@
-name: MultiQC
-description: Aggregate results from bioinformatics analyses across many samples into a single report
-keywords:
-    - QC
-    - bioinformatics tools
-    - Beautiful stand-alone HTML report
-tools:
-    - fastqc:
-        description: |
-            MultiQC searches a given directory for analysis logs and compiles a HTML report.
-            It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
-        homepage: https://multiqc.info/
-        documentation: https://multiqc.info/docs/
-input:
-    -
-        - reads:
-            type: file
-            description: List of report file(s)
-output:
-    -
-        - multiqc_report:
-            type: file
-            description: MultiQC report
-            pattern: "*multiqc*.html"
-authors:
-    - "@FelixKrueger"

deprecated/multiqc/test/input/bowtie2/test_GRCm38_bowtie2_stats.txt

@@ -1 +0,0 @@
-../../../../bowtie2/test/output/test_GRCm38_bowtie2_stats.txt

deprecated/multiqc/test/input/fastq_screen/test_R1_screen.txt

@@ -1 +0,0 @@
-../../../../fastq_screen/test/output/test_R1_screen.txt

deprecated/multiqc/test/input/fastqc/test_R1_fastqc.zip

@@ -1 +0,0 @@
-../../../../fastqc/test/output/test_R1_fastqc.zip

deprecated/multiqc/test/input/fastqc/test_R1_val_1_fastqc.zip

@@ -1 +0,0 @@
-../../../../fastqc/test/output/test_R1_val_1_fastqc.zip

deprecated/multiqc/test/input/fastqc/test_R2_fastqc.zip

@@ -1 +0,0 @@
-../../../../fastqc/test/output/test_R2_fastqc.zip

deprecated/multiqc/test/input/fastqc/test_R2_val_2_fastqc.zip

@@ -1 +0,0 @@
-../../../../fastqc/test/output/test_R2_val_2_fastqc.zip

deprecated/multiqc/test/input/hisat2/Ecoli_DNA_R_E_coli_hisat2_stats.txt

@@ -1 +0,0 @@
-../../../../hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

deprecated/multiqc/test/input/trim_galore/test_R1.fastq.gz_trimming_report.txt

@@ -1 +0,0 @@
-../../../../trim_galore/test/output/test_R1.fastq.gz_trimming_report.txt

deprecated/multiqc/test/input/trim_galore/test_R2.fastq.gz_trimming_report.txt

@@ -1 +0,0 @@
-../../../../trim_galore/test/output/test_R2.fastq.gz_trimming_report.txt

deprecated/multiqc/test/main.nf

@@ -1,44 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl=2
-
-params.outdir = "."
-params.verbose = false
-params.multiqc_args = ''
-
-// include '../../../tests/functions/check_process_outputs.nf'
-include '../main.nf'
-
-if (params.verbose){
-    println ("[WORKFLOW] MULTIQC ARGS: "          + params.multiqc_args)
-}
-
-multiqc_ch = Channel
-  .fromPath( ['../../../test-datasets/*trimming_report.txt','../../../test-datasets/*fastqc.zip','../../../test-datasets/*screen.txt','../../../test-datasets/*bowtie2_stats.txt'] )
-  .collect()   // collect() flattens all channels to single list
-  // .view()   // view the files in the channel
-  
-
-// Run the workflow
-workflow {
-
-    main:
-        // This is an example workflow for real reads aligned with Bowtie2. Just for illustration purposes
-        
-        // FASTQC          (file_ch, params.outdir, params.fastqc_args, params.verbose)
-        // FASTQ_SCREEN    (file_ch, params.outdir, params.fastq_screen_args, params.verbose)
-        // TRIM_GALORE     (file_ch, params.outdir, params.trim_galore_args, params.verbose)
-        // FASTQC2         (TRIM_GALORE.out.reads, params.outdir, params.fastqc_args, params.verbose)
-        // BOWTIE2         (TRIM_GALORE.out.reads, params.outdir, params.bowtie2_args, params.verbose)
-     
-        // merging channels for MultiQC
-        // multiqc_ch = FASTQC.out.report.mix(
-        //     TRIM_GALORE.out.report,
-        //     FASTQ_SCREEN.out.report,
-        //     FASTQC2.out.report,
-        //     BOWTIE2.out.stats,
-        // ).collect()     
-
-        MULTIQC                          (multiqc_ch, params.outdir, params.multiqc_args, params.verbose)
-
-        // .check_output() TODO
-}

deprecated/multiqc/test/nextflow.config

@@ -1,2 +0,0 @@
-// docker.enabled = true
-params.outdir = './results'

deprecated/samtools/faidx/main.nf

@@ -1,16 +0,0 @@
-process samtools_faidx {
-    tag "$fasta"
-
-    container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
-
-    input:
-        path fasta
-
-    output:
-        path "${fasta}.fai"
-
-    script:
-    """
-    samtools faidx ${fasta}
-    """
-}

deprecated/samtools/faidx/meta.yml

@@ -1,27 +0,0 @@
-name: samtools faidx
-description: index a fasta file
-keywords:
-    - faidx
-tools:
-    - samtools:
-        description: |
-            SAMtools is a set of utilities for interacting with and post-processing
-            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
-            These files are generated as output by short read aligners like BWA.
-        homepage: http://www.htslib.org/
-        documentation: hhttp://www.htslib.org/doc/samtools.html
-        doi: 10.1093/bioinformatics/btp352
-input:
-    -
-        - input:
-            type: file
-            description: Input fasta file
-            pattern: "*.{fasta,fa}"
-output:
-    -
-        - faidx:
-            type: file
-            description: samtools index fasta file
-            pattern: "*.fasta.fai"
-authors:
-    - "@maxulysse"

deprecated/samtools/faidx/test/main.nf

@@ -1,13 +0,0 @@
-#!/usr/bin/env nextflow
-nextflow.preview.dsl = 2
-include '../../../tests/functions/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
-
-// Define input channels
-input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
-
-// Run the workflow
-workflow {
-    samtools_faidx(input)
-    // .check_output()
-}

deprecated/samtools/faidx/test/nextflow.config

@@ -1,2 +0,0 @@
-docker.enabled = true
-params.outdir = './results'

deprecated/umi_tools/Dockerfile

@@ -1,8 +0,0 @@
-FROM nfcore/base:1.7
-LABEL authors="chris.cheshire@crick.ac.uk" \
-    description="Docker image containing all requirements for the nf-core umi_tools module"
-
-# Install conda packages
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nfcore-module-umitools/bin:$PATH

deprecated/umi_tools/environment.yml

@@ -1,10 +0,0 @@
-# This file creates a conda environment for the umi_tools module
-#   conda env create -f environment.yml
-name: nfcore-module-umitools
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - umi_tools=1.0.1
-  - samtools=1.1.0

deprecated/umi_tools/main.nf

@@ -1,45 +0,0 @@
-#!/usr/bin/env nextflow
-
-// Specify DSL2
-nextflow.preview.dsl = 2
-
-// Process definition
-process umitools_dedup {
-    publishDir "${params.outdir}/umitools/dedup",
-        mode: "copy", overwrite: true
-
-    container 'luslab/nf-modules-umitools:latest'
-
-    input:
-        tuple val(sample_id), path(bam)
-
-    output:
-        tuple val(sample_id), path("${sample_id}.dedup.bam"), emit: dedupBam
-        tuple val(sample_id), path("${sample_id}.dedup.bam.bai"), emit: dedupBai
-        path "*.dedup.log", emit: report
-
-    script:
-
-    // Init
-    args = "--log=${sample_id}.dedup.log"
-
-    // Check main args string exists and strip whitespace
-    if(params.umitools_dedup_args) {
-        ext_args = params.umitools_dedup_args
-        args += " " + ext_args.trim()
-    }
-
-    // Contruct CL line
-    dedup_command = "umi_tools dedup ${args} -I ${bam[0]} -S ${sample_id}.dedup.bam --output-stats=${sample_id}"
-
-    // Log
-    if (params.verbose){
-        println ("[MODULE] umi_tools/dedup command: " + dedup_command)
-    }
-
-    //SHELL
-    """
-    ${dedup_command}
-    samtools index ${sample_id}.dedup.bam
-    """
-}