Standardise file names using only underscore

assets/multiqc_config.yml

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

conf/modules.config

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