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Update parameter names

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This commit is contained in:
James Fellows Yates 2022-05-31 20:11:19 +02:00
parent 792e2d019b
commit 16ec5bf74a
6 changed files with 16 additions and 15 deletions
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8
conf/modules.config
View file

@ -54,7 +54,7 @@ process {
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "", params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "", params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
// filtering options // filtering options
"--length_required ${params.shortread_clipmerge_minlength}", "--length_required ${params.shortread_qc_minlength}",
(params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' (params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp') ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
@ -75,7 +75,7 @@ process {
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "", params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe", params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
// filtering options // filtering options
"--length_required ${params.shortread_clipmerge_minlength}", "--length_required ${params.shortread_qc_minlength}",
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
@ -141,9 +141,9 @@ process {
"--target_bases ${params.longread_qc_targetnbases}" "--target_bases ${params.longread_qc_targetnbases}"
] ]
.join(' ').trim() .join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
publishDir = [ publishDir = [
path: { "${params.outdir}/porechop" }, path: { "${params.outdir}/filtlong" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
pattern: '*.fastq.gz', pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads enabled: params.save_preprocessed_reads

4
conf/test_nopreprocessing.config
View file

@ -24,8 +24,8 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed // TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = false perform_shortread_qc = false
perform_longread_clip = false perform_longread_qc = false
perform_shortread_complexityfilter = false perform_shortread_complexityfilter = false
perform_shortread_hostremoval = false perform_shortread_hostremoval = false
perform_longread_hostremoval = false perform_longread_hostremoval = false

4
conf/test_noprofiling.config
View file

@ -24,8 +24,8 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed // TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv' input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv' databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = true perform_shortread_qc = true
perform_longread_clip = true perform_longread_qc = true
perform_shortread_complexityfilter = true perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true perform_shortread_hostremoval = true
perform_longread_hostremoval = true perform_longread_hostremoval = true

2
modules.json
View file

@ -37,7 +37,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
}, },
"filtlong": { "filtlong": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d" "git_sha": "723852bf3d3b12059b2f53da8bc055206f3019d7"
}, },
"kaiju/kaiju": { "kaiju/kaiju": {
"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe" "git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"

7
modules/nf-core/modules/filtlong/main.nf generated
View file

@ -11,7 +11,7 @@ process FILTLONG {
tuple val(meta), path(shortreads), path(longreads) tuple val(meta), path(shortreads), path(longreads)
output: output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads tuple val(meta), path("*.fastq.gz"), emit: reads
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -20,13 +20,14 @@ process FILTLONG {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}" def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
if ("$longreads" == "${prefix}.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
""" """
filtlong \\ filtlong \\
$short_reads \\ $short_reads \\
$args \\ $args \\
$longreads \\ $longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz | gzip -n > ${prefix}.fastq.gz
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
"${task.process}": "${task.process}":

6
workflows/taxprofiler.nf
View file

@ -20,11 +20,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' } if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
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." 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."
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" 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"
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" 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"
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'" 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'"
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." } 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." }
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." } 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." }