Merge branch 'nf-core:dev' into update_output

assets/multiqc_config.yml

@@ -19,9 +19,10 @@ custom_logo_title: "nf-core/taxprofiler"
 run_modules:
   - fastqc
   - adapterRemoval
+  - fastp
   - bbduk
   - prinseqplusplus
-  - fastp
+  - porechop
   - filtlong
   - bowtie2
   - minimap2
@@ -32,9 +33,13 @@ run_modules:
   - diamond
   - malt
   - motus
-  - porechop
   - custom_content
 
+sp:
+  diamond:
+    contents: "diamond v"
+    num_lines: 10
+
 #extra_fn_clean_exts:
 #    - '_fastp'
 #    - '.pe.settings'
@@ -102,9 +107,10 @@ table_columns_placement:
   FastQC (pre-Trimming):
     total_sequences: 100
     avg_sequence_length: 110
-    percent_duplicates: 120
+    median_sequence_length: 120
-    percent_gc: 130
+    percent_duplicates: 130
-    percent_fails: 140
+    percent_gc: 140
+    percent_fails: 150
   Falco (pre-Trimming):
     total_sequences: 200
     avg_sequence_length: 210
@@ -118,43 +124,84 @@ table_columns_placement:
     after_filtering_gc_content: 330
     after_filtering_q30_rate: 340
     after_filtering_q30_bases: 350
+    filtering_result_passed_filter_reads: 360
   Adapter Removal:
     aligned_total: 360
     percent_aligned: 370
     percent_collapsed: 380
     percent_discarded: 390
+  Porechop:
+    Input Reads: 400
+    Start Trimmed: 410
+    Start Trimmed Percent: 420
+    End Trimmed: 430
+    End Trimmed Percent: 440
+    Middle Split: 450
+    Middle Split Percent: 460
+  Filtlong:
+    Target bases: 500
   FastQC (post-Trimming):
-    total_sequences: 400
+    total_sequences: 600
-    avg_sequence_length: 410
+    avg_sequence_length: 610
-    percent_duplicates: 420
+    median_sequence_length: 620
-    percent_gc: 430
+    percent_duplicates: 630
-    percent_fails: 440
+    percent_gc: 640
+    percent_fails: 650
   Falco (post-Trimming):
-    total_sequences: 500
+    total_sequences: 700
-    avg_sequence_length: 510
+    avg_sequence_length: 710
-    percent_duplicates: 520
+    percent_duplicates: 720
-    percent_gc: 530
+    percent_gc: 730
-    percent_fails: 540
+    percent_fails: 740
+  BBDuk:
+    Input reads: 800
+    Total Removed bases percent: 810
+    Total Removed bases: 820
+    Total Removed reads percent: 830
+    Total Removed reads: 840
+  PRINSEQ++:
+    prinseqplusplus_total: 900
   bowtie2:
-    overall_alignment_rate: 600
+    overall_alignment_rate: 1000
   Samtools Stats:
-    raw_total_sequences: 700
+    raw_total_sequences: 1100
-    reads_mapped: 710
+    reads_mapped: 1110
-    reads_mapped_percent: 720
+    reads_mapped_percent: 1120
-    reads_properly_paired_percent: 730
+    reads_properly_paired_percent: 1130
-    non-primary_alignments: 740
+    non-primary_alignments: 1140
-    reads_MQ0_percent: 750
+    reads_MQ0_percent: 1150
-    error_rate: 760
+    error_rate: 1160
-  MALT:
+  Bracken:
-    Num. of queries: 1000
+    "% Unclassified": 1200
-    Total reads: 1100
+    "% Top 5": 1210
-    Mappability: 1200
+  Centrifuge:
-    Assig. Taxonomy: 1300
+    "% Unclassified": 1300
-    Taxonomic assignment success: 1400
+    "% Top 5": 1310
+  DIAMOND:
+    queries_aligned: 1400
   Kaiju:
-    assigned: 2000
+    assigned: 1500
-    "% Assigned": 2100
+    "% Assigned": 1510
-    "% Unclassified": 2200
+    "% Unclassified": 1520
+  Kraken:
+    "% Unclassified": 1600
+    "% Top 5": 1610
+  MALT:
+    "Num. of queries": 1700
+    Total reads: 1710
+    Mappability: 1720
+    Assig. Taxonomy: 1730
+    Taxonomic assignment success: 1740
+  motus:
+    Total number of reads: 1800
+    Number of reads after filtering: 1810
+    Total number of inserts: 1820
+    Unique mappers: 1830
+    Multiple mappers: 1840
+    Ignored multiple mapper without unique hit: 1850
+    "Number of ref-mOTUs": 1860
+    "Number of meta-mOTUs": 1870
+    "Number of ext-mOTUs": 1880
 
 table_columns_visible:
   FastQC (pre-Trimming):
@@ -176,6 +223,16 @@ table_columns_visible:
     after_filtering_gc_content: False
     after_filtering_q30_rate: False
     after_filtering_q30_bases: False
+  porechop:
+    Input reads: False
+    Start Trimmed:
+    Start Trimmed Percent: True
+    End Trimmed: False
+    End Trimmed Percent: True
+    Middle Split: False
+    Middle Split Percent: True
+  Filtlong:
+    Target bases: True
   Adapter Removal:
     aligned_total: True
     percent_aligned: True
@@ -193,6 +250,14 @@ table_columns_visible:
     percent_duplicates: False
     percent_gc: False
     percent_fails: False
+  BBDuk:
+    Input reads: False
+    Total Removed bases Percent: False
+    Total Removed bases: False
+    Total Removed reads percent: True
+    Total Removed reads: False
+  "PRINSEQ++":
+    prinseqplusplus_total: True
   bowtie2:
     overall_alignment_rate: True
   Samtools Stats:
@@ -204,24 +269,35 @@ table_columns_visible:
     reads_MQ0_percent: False
     error_rate: False
   Kraken:
-    "% Unclassified": True
+    "% Unclassified": False
     "% Top 5": False
   Bracken:
-    "% Unclassified": True
+    "% Unclassified": False
     "% Top 5": False
-  Centrifuge:
+  Centrifuge: False
-    "% Unclassified": True
+  DIAMOND:
-    "% Top 5": False
+    queries_aligned: False
-  MALT:
-    Num. of queries: True
-    Total reads: True
-    Mappability: True
-    Assig. Taxonomy: False
-    Taxonomic assignment success: True
   Kaiju:
     assigned: False
     "% Assigned": False
-    "% Unclassified": True
+    "% Unclassified": False
+  MALT:
+    "Num. of queries": False
+    Total reads: False
+    Mappability: False
+    Assig. Taxonomy: False
+    Taxonomic assignment success: False
+  motus:
+    Total number of reads: False
+    Number of reads after filtering: False
+    Total number of inserts: False
+    Unique mappers: False
+    Multiple mappers: False
+    Ignored multiple mapper without unique hit: False
+    "Number of ref-mOTUs": False
+    "Number of meta-mOTUs": False
+    "Number of ext-mOTUs": False
+
 table_columns_name:
   FastQC (pre-Trimming):
     total_sequences: "Nr. Input Reads"
@@ -253,7 +329,13 @@ table_columns_name:
     reads_mapped_percent: "% Mapped Reads"
 
 extra_fn_clean_exts:
-  - ".kraken2.kraken2.report.txt"
+  - "kraken2.report.txt"
-  - ".centrifuge.txt"
+  - ".txt"
-  - ".bracken.kraken2.report.txt"
   - ".settings"
+  - ".bbduk"
+  - ".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/" },
@@ -300,9 +300,8 @@ process {
         ext.args =  [
                 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",
-                "-VERBOSE 2"
             ].join(' ').trim()
-        ext.prefix = { "${meta.id}-${meta.run_accession}" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             [
                 path: { "${params.outdir}/prinseqplusplus/" },
@@ -351,7 +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}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        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,
@@ -361,7 +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,
@@ -390,7 +389,7 @@ process {
     withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
         ext.args = { "${meta.db_params}" }
         // one run with multiple samples, so fix ID to just db name to ensure clean log name
-        ext.prefix = { "${meta.db_name}" }
+        ext.prefix = { "${meta.db_name}.krakenuniq" }
         publishDir = [
             path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -399,7 +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,
@@ -408,7 +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,
@@ -418,12 +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,
@@ -433,7 +432,7 @@ process {
 
     withName: METAPHLAN3_METAPHLAN3 {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan3" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan3" }
         publishDir = [
             path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -457,13 +456,13 @@ process {
             pattern: '*.{txt,sam,gz}'
         ]
         ext.args = { "${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,
@@ -481,7 +480,7 @@ process {
     }
 
     withName: KAIJU_KAIJU {
-        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}_${meta.db_name}.kaiju" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaiju" }
         publishDir = [
             path: { "${params.outdir}/kaiju/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -505,7 +504,7 @@ process {
 
     withName: DIAMOND_BLASTX {
         ext.args = { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.diamond" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.diamond" }
         publishDir = [
             path: { "${params.outdir}/diamond/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -521,7 +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

modules.json

@@ -173,7 +173,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
                         "installed_by": ["modules"]
                     },
                     "porechop/porechop": {

modules/nf-core/multiqc/main.nf

@@ -1,10 +1,10 @@
 process MULTIQC {
     label 'process_single'
 
-    conda "bioconda::multiqc=1.13"
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"