mirror of
https://github.com/MillironX/taxprofiler.git
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Add samtools stats for long-reads
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parent
bf89525bc2
commit
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8 changed files with 231 additions and 0 deletions
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@ -21,6 +21,7 @@ run_modules:
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- adapterRemoval
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- fastp
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- bowtie2
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- samtools
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- kraken
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- malt
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- custom_content
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@ -153,6 +153,14 @@
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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48
modules/nf-core/samtools/index/main.nf
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48
modules/nf-core/samtools/index/main.nf
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@ -0,0 +1,48 @@
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process SAMTOOLS_INDEX {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("*.bai") , optional:true, emit: bai
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tuple val(meta), path("*.csi") , optional:true, emit: csi
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tuple val(meta), path("*.crai"), optional:true, emit: crai
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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"""
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samtools \\
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index \\
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-@ ${task.cpus-1} \\
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$args \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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stub:
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"""
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touch ${input}.bai
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touch ${input}.crai
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touch ${input}.csi
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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53
modules/nf-core/samtools/index/meta.yml
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53
modules/nf-core/samtools/index/meta.yml
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name: samtools_index
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description: Index SAM/BAM/CRAM file
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keywords:
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- index
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- bam
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- sam
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- cram
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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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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bai:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- crai:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- csi:
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type: file
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description: CSI index file
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pattern: "*.{csi}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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- "@ewels"
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- "@maxulysse"
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49
modules/nf-core/samtools/stats/main.nf
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49
modules/nf-core/samtools/stats/main.nf
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@ -0,0 +1,49 @@
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process SAMTOOLS_STATS {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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path fasta
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output:
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tuple val(meta), path("*.stats"), emit: stats
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "--reference ${fasta}" : ""
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"""
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samtools \\
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stats \\
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--threads ${task.cpus} \\
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${reference} \\
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${input} \\
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> ${prefix}.stats
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.stats
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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53
modules/nf-core/samtools/stats/meta.yml
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53
modules/nf-core/samtools/stats/meta.yml
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name: samtools_stats
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description: Produces comprehensive statistics from SAM/BAM/CRAM file
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keywords:
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- statistics
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- counts
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- bam
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- sam
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- cram
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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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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
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description: BAM/CRAM file from alignment
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAI/CRAI file from alignment
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pattern: "*.{bai,crai}"
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- fasta:
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type: optional file
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description: Reference file the CRAM was created with
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pattern: "*.{fasta,fa}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- stats:
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type: file
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description: File containing samtools stats output
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pattern: "*.{stats}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@drpatelh"
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- "@FriederikeHanssen"
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@ -6,6 +6,8 @@ include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/inde
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include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
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include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
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include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main'
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include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
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include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
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workflow LONGREAD_HOSTREMOVAL {
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take:
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@ -39,9 +41,22 @@ workflow LONGREAD_HOSTREMOVAL {
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SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
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ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
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SAMTOOLS_INDEX ( SAMTOOLS_VIEW.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
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SAMTOOLS_VIEW.out.bam
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.join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
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.set { bam_bai }
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SAMTOOLS_STATS ( bam_bai, reference )
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ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_STATS.out.stats )
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emit:
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stats = SAMTOOLS_STATS.out.stats //channel: [val(meta), [reads ] ]
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reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
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versions = ch_versions // channel: [ versions.yml ]
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mqc = ch_multiqc_files
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}
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@ -281,6 +281,10 @@ workflow TAXPROFILER {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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if (params.perform_longread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) )
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if ( params.run_profile_standardisation ) {
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