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https://github.com/MillironX/taxprofiler.git
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Update parameter names
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parent
792e2d019b
commit
16ec5bf74a
6 changed files with 16 additions and 15 deletions
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@ -54,7 +54,7 @@ process {
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params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
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params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}",
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"--length_required ${params.shortread_qc_minlength}",
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(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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@ -75,7 +75,7 @@ process {
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params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
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params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}",
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"--length_required ${params.shortread_qc_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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@ -141,9 +141,9 @@ process {
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"--target_bases ${params.longread_qc_targetnbases}"
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]
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.join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
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publishDir = [
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path: { "${params.outdir}/porechop" },
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path: { "${params.outdir}/filtlong" },
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mode: params.publish_dir_mode,
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pattern: '*.fastq.gz',
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enabled: params.save_preprocessed_reads
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@ -24,8 +24,8 @@ params {
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = false
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perform_longread_clip = false
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perform_shortread_qc = false
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perform_longread_qc = false
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perform_shortread_complexityfilter = false
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perform_shortread_hostremoval = false
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perform_longread_hostremoval = false
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@ -24,8 +24,8 @@ params {
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_clipmerge = true
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perform_longread_clip = true
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perform_shortread_qc = true
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perform_longread_qc = true
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perform_shortread_complexityfilter = true
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perform_shortread_hostremoval = true
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perform_longread_hostremoval = true
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@ -37,7 +37,7 @@
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"filtlong": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "723852bf3d3b12059b2f53da8bc055206f3019d7"
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},
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"kaiju/kaiju": {
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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7
modules/nf-core/modules/filtlong/main.nf
generated
7
modules/nf-core/modules/filtlong/main.nf
generated
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@ -11,7 +11,7 @@ process FILTLONG {
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tuple val(meta), path(shortreads), path(longreads)
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output:
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tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
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tuple val(meta), path("*.fastq.gz"), emit: reads
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path "versions.yml" , emit: versions
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when:
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@ -20,13 +20,14 @@ process FILTLONG {
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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 short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
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"""
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filtlong \\
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$short_reads \\
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$args \\
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$longreads \\
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| gzip -n > ${prefix}_lr_filtlong.fastq.gz
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| gzip -n > ${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -20,11 +20,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
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if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
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if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
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if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
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if ( (params.longread_qc_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter requested but quality-control not turned on. Please specify --perform_long_qc"
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_clipmerge == false || params.shortread_clipmerge_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_clipmerge and/or --shortread_clipmerge_tool 'fastp'"
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if (params.shortread_complexityfilter_tool == 'fastp' && ( params.perform_shortread_qc == false || params.shortread_qc_tool != 'fastp' )) exit 1, "ERROR: [nf-core/taxprofiler] cannot use fastp complexity filtering if preprocessing not turned on and/or tool is not fastp. Please specify --perform_shortread_qc and/or --shortread_qc_tool 'fastp'"
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if (params.perform_shortread_hostremoval && !params.hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --hostremoval_reference FASTA supplied. Check input." }
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if (!params.hostremoval_reference && params.hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --hostremoval_reference FASTA supplied. Check input." }
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