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https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Remove some more modules
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drpatelh
parent
1edc58a36b
commit
4f590ff239
16 changed files with 0 additions and 240 deletions
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@ -1,16 +0,0 @@
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process bwa_index {
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tag "$fasta"
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container 'quay.io/biocontainers/bwa:0.7.17--hed695b0_7'
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input:
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path fasta
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output:
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path "${fasta}.*"
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script:
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"""
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bwa index ${fasta}
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"""
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}
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name: bwa index
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description: create indexes for BWA from a fasta file
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keywords:
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- index
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tools:
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- bwa:
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description: |
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BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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input:
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-
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- input:
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type: file
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description: Input fasta file
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pattern: "*.{fasta,fa}"
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output:
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-
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- index:
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type: file
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description: bwa indexes file
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pattern: "*.{fasta,fa}.{amb,ann,bwt,pac,sa}"
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authors:
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- "@maxulysse"
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#!/usr/bin/env nextflow
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nextflow.preview.dsl = 2
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include '../../../tests/functions/check_process_outputs.nf' params(params)
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include '../main.nf' params(params)
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// Define input channels
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input = '../../../test-datasets/tools/bwa/index/input/reference.fasta'
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Channel
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.from(input)
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.set { ch_input }
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// Run the workflow
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workflow {
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fastqc(ch_input)
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// .check_output()
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}
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docker.enabled = true
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params.outdir = './results'
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@ -1,7 +0,0 @@
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FROM nfcore/base
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LABEL authors="Jeremy Guntoro" \
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description="Docker image containing all requirements for nf-core/modules/bwa/mem module"
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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ENV PATH /opt/conda/envs/nf-core-bwa-mem/bin:$PATH
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# You can use this file to create a conda environment for this pipeline:
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# conda env create -f environment.yml
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name: nf-core-bwa-mem
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- bioconda::bwa=0.7.17
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- bioconda::samtools=1.9
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params.bwa_options = "-M -B 2"
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params.sequencer = "ILLUMINA"
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process bwa_mem {
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tag "$id"
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publishDir "${params.outdir}/bwa_mem", mode: 'copy'
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//TO-DO: Change container declaration, for now a test container is present in my personal docker acccount
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container 'jeremy1805/bwa-mem-img'
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input:
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tuple val(id), path(reads)
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path genomeindex
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val indexprefix
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output:
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tuple path("*.bam"), path("*.bai")
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script:
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"""
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bwa mem -t ${task.cpus} -R "@RG\\tID:${id}\\tLB:${id}\\tSM:${id}\\tPL:${params.sequencer}" \\
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${params.bwa_options} ${indexprefix} ${reads} | samtools sort -@8 -O BAM -o ${id}.bam -
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samtools index ${id}.bam
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"""
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}
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name: bwa mem
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description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
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keywords:
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- mem
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- bwa
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- alignment
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tools:
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- bwa:
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description: |
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BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
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homepage: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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input:
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-
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- id:
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type: val
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description: read/read pair id
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- reads:
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type: file
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description: Input fastq file
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pattern: "*.{fastq,fq}"
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- index:
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type: file
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description: bwa indexes file
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pattern: "*.{amb,ann,bwt,pac,sa}"
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- prefix:
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type: val
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description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
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output:
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-
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- bam:
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type: file
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description: Output bam file
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pattern: "*.bam"
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- bamindex:
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type: file
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description: Output bam index file
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pattern: "*.bai"
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authors:
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- "@jeremy1805"
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@ -1,13 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.preview.dsl = 2
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include '../../../../tests/functions/check_process_outputs.nf' params(params)
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include '../main.nf' params(params)
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reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
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index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
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prefix = 'H3N2'
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workflow {
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read_input=Channel.fromFilePairs(reads)
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bwa_mem(read_input,file(index),prefix)
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}
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docker.enabled = true
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params.outdir = './results'
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@ -1,8 +0,0 @@
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FROM nfcore/base:1.7
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LABEL authors="phil.ewels@scilifelab.se" \
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description="Docker image for nf-core modules samtools"
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# foobar
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COPY environment.yml /
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RUN conda env create -f /environment.yml && conda clean -a
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ENV PATH /opt/conda/envs/nf-core-modules-samtools/bin:$PATH
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@ -1,9 +0,0 @@
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# You can use this file to create a conda environment for this pipeline:
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# conda env create -f environment.yml
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name: nf-core-modules-samtools
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- samtools=1.9
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@ -1,21 +0,0 @@
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process samtools_index {
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tag "${bam.baseName}"
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container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
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input:
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path bam
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output:
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path "*.bai"
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script:
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def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
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def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
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"""
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samtools index $bam \\
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-@ ${task.cpus} ${avail_mem}
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samtools --version &> v_samtools.txt
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"""
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}
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name: samtools index
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description: index a BAM or CRAM file
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keywords:
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- index
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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input:
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-
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- input:
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type: file
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description: Input BAM or CRAM file
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pattern: "*.{bam,cram}"
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output:
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-
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- index:
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type: file
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description: BAM or CRAM index file
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pattern: "*.{bai}"
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authors:
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- "@ewels"
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@ -1,13 +0,0 @@
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#!/usr/bin/env nextflow
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echo true
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cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
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process sayHello {
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input:
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val x from cheers
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script:
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"""
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echo '$x world!'
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"""
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}
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docker.enabled = true
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params.outdir = './results'
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