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update MultiQC and include latest modules

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This commit is contained in:
James Fellows Yates 2023-01-16 14:39:52 +01:00
parent 6dcf619518
commit d6fa45b500
4 changed files with 94 additions and 45 deletions
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130
assets/multiqc_config.yml
View file

@ -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
percent_gc: 130
percent_fails: 140
median_sequence_length: 120
percent_duplicates: 130
percent_gc: 140
percent_fails: 150
Falco (pre-Trimming):
total_sequences: 200
avg_sequence_length: 210
@ -118,43 +124,63 @@ 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
avg_sequence_length: 410
percent_duplicates: 420
percent_gc: 430
percent_fails: 440
total_sequences: 600
avg_sequence_length: 610
median_sequence_length: 620
percent_duplicates: 630
percent_gc: 640
percent_fails: 650
Falco (post-Trimming):
total_sequences: 500
avg_sequence_length: 510
percent_duplicates: 520
percent_gc: 530
percent_fails: 540
total_sequences: 700
avg_sequence_length: 710
percent_duplicates: 720
percent_gc: 730
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
reads_mapped: 710
reads_mapped_percent: 720
reads_properly_paired_percent: 730
non-primary_alignments: 740
reads_MQ0_percent: 750
error_rate: 760
raw_total_sequences: 1100
reads_mapped: 1110
reads_mapped_percent: 1120
reads_properly_paired_percent: 1130
non-primary_alignments: 1140
reads_MQ0_percent: 1150
error_rate: 1160
MALT:
Num. of queries: 1000
Total reads: 1100
Mappability: 1200
Assig. Taxonomy: 1300
Taxonomic assignment success: 1400
"Num. of queries": 1200
Total reads: 1210
Mappability: 1220
Assig. Taxonomy: 1230
Taxonomic assignment success: 1240
Kaiju:
assigned: 2000
"% Assigned": 2100
"% Unclassified": 2200
assigned: 1300
"% Assigned": 1310
"% Unclassified": 1320
table_columns_visible:
FastQC (pre-Trimming):
@ -176,6 +202,16 @@ 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 +229,14 @@ 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:
@ -212,16 +256,19 @@ table_columns_visible:
Centrifuge:
"% Unclassified": True
"% Top 5": False
MALT:
Num. of queries: True
Total reads: True
Mappability: True
Assig. Taxonomy: False
Taxonomic assignment success: True
DIAMOND:
queries_aligned: True
Kaiju:
assigned: False
"% Assigned": False
"% Unclassified": True
MALT:
"Num. of queries": True
Total reads: True
Mappability: True
Assig. Taxonomy: False
Taxonomic assignment success: True
table_columns_name:
FastQC (pre-Trimming):
total_sequences: "Nr. Input Reads"
@ -253,7 +300,10 @@ table_columns_name:
reads_mapped_percent: "% Mapped Reads"
extra_fn_clean_exts:
- ".kraken2.kraken2.report.txt"
- ".centrifuge.txt"
- ".bracken.kraken2.report.txt"
- "kraken2.report.txt"
- ".txt"
- ".settings"
- ".bbduk"
- ".unmapped"
- "_filtered"
- "_processed"

1
conf/modules.config
View file

@ -300,7 +300,6 @@ 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}" }
publishDir = [

2
modules.json
View file

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

6
modules/nf-core/multiqc/main.nf generated
View file

@ -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' :
'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"