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Code Issues Releases Packages Activity

Standardise file names using only underscore

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This commit is contained in:
James Fellows Yates 2023-01-17 10:58:30 +01:00
parent 480248bcfd
commit 92dff9b453
2 changed files with 17 additions and 14 deletions
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3
assets/multiqc_config.yml
View file

@ -336,3 +336,6 @@ extra_fn_clean_exts:
- ".unmapped" - ".unmapped"
- "_filtered" - "_filtered"
- "_processed" - "_processed"
section_comments:
general_stats: "By default, all read count columns are displayed as millions (M) of reads."

28
conf/modules.config
View file

@ -280,7 +280,7 @@ process {
"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}", "entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f" params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
[ [
path: { "${params.outdir}/bbduk/" }, path: { "${params.outdir}/bbduk/" },
@ -301,7 +301,7 @@ process {
params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}", params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0", "-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}-${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
[ [
path: { "${params.outdir}/prinseqplusplus/" }, path: { "${params.outdir}/prinseqplusplus/" },
@ -350,7 +350,7 @@ process {
withName: KRAKEN2_KRAKEN2 { withName: KRAKEN2_KRAKEN2 {
ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" } ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}.kraken" } ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}_${meta.db_name}.bracken" : "${meta.id}_${meta.db_name}.kraken" } : { meta.tool == "bracken" ? "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" : "${meta.id}_${meta.run_accession}_${meta.db_name}.kraken" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kraken2/${meta.db_name}/" }, path: { "${params.outdir}/kraken2/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -360,7 +360,7 @@ process {
withName: BRACKEN_BRACKEN { withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore' errorStrategy = 'ignore'
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [ publishDir = [
path: { "${params.outdir}/bracken/${meta.db_name}/" }, path: { "${params.outdir}/bracken/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -398,7 +398,7 @@ process {
} }
withName: KRONA_CLEANUP { withName: KRONA_CLEANUP {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/krona/" }, path: { "${params.outdir}/krona/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -407,7 +407,7 @@ process {
} }
withName: KRONA_KTIMPORTTEXT { withName: KRONA_KTIMPORTTEXT {
ext.prefix = { "${meta.tool}-${meta.id}" } ext.prefix = { "${meta.tool}_${meta.id}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/krona/" }, path: { "${params.outdir}/krona/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -417,12 +417,12 @@ process {
withName: 'MEGAN_RMA2INFO_KRONA' { withName: 'MEGAN_RMA2INFO_KRONA' {
ext.args = { "--read2class Taxonomy" } ext.args = { "--read2class Taxonomy" }
ext.prefix = { "${meta.id}-${meta.db_name}" } ext.prefix = { "${meta.id}_${meta.db_name}" }
} }
withName: KRONA_KTIMPORTTAXONOMY { withName: KRONA_KTIMPORTTAXONOMY {
ext.args = "-i" ext.args = "-i"
ext.prefix = { "${meta.tool}-${meta.id}" } ext.prefix = { "${meta.tool}_${meta.id}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/krona/" }, path: { "${params.outdir}/krona/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -432,7 +432,7 @@ process {
withName: METAPHLAN3_METAPHLAN3 { withName: METAPHLAN3_METAPHLAN3 {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.metaphlan3" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.metaphlan3" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan3" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan3" }
publishDir = [ publishDir = [
path: { "${params.outdir}/metaphlan3/${meta.db_name}/" }, path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -456,13 +456,13 @@ process {
pattern: '*.{txt,sam,gz}' pattern: '*.{txt,sam,gz}'
] ]
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
} }
withName: CENTRIFUGE_KREPORT { withName: CENTRIFUGE_KREPORT {
errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'} errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.centrifuge" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.centrifuge" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
publishDir = [ publishDir = [
path: { "${params.outdir}/centrifuge/${meta.db_name}/" }, path: { "${params.outdir}/centrifuge/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -480,7 +480,7 @@ process {
} }
withName: KAIJU_KAIJU { withName: KAIJU_KAIJU {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.kaiju" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.kaiju" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
publishDir = [ publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" }, path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -504,7 +504,7 @@ process {
withName: DIAMOND_BLASTX { withName: DIAMOND_BLASTX {
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.diamond" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.diamond" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.diamond" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
publishDir = [ publishDir = [
path: { "${params.outdir}/diamond/${meta.db_name}/" }, path: { "${params.outdir}/diamond/${meta.db_name}/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
@ -520,7 +520,7 @@ process {
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : "" params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ") ].join(',').replaceAll(','," ")
} }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}/" }, path: { "${params.outdir}/motus/${meta.db_name}/" },
mode: params.publish_dir_mode mode: params.publish_dir_mode