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Merge pull request #253 from nf-core/futher-further-prerelease-updates

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Futher further prerelease updates: FALCO display in MultiQC
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Sofia Stamouli 2023-03-06 15:56:50 +01:00 committed by GitHub
commit d647e61a2f
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5 changed files with 64 additions and 97 deletions
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103
assets/multiqc_config.yml
View file

@ -39,6 +39,10 @@ sp:
diamond:
contents: "diamond v"
num_lines: 10
fastqc/data:
fn_re: ".*(fastqc|falco)_data.txt$"
fastqc/zip:
fn: "*_fastqc.zip"
#extra_fn_clean_exts:
# - '_fastp'
@ -47,25 +51,23 @@ sp:
top_modules:
- "fastqc":
name: "FastQC (pre-Trimming)"
name: "FastQC / Falco (pre-Trimming)"
path_filters:
- "*raw_*fastqc.zip"
- "*raw*"
path_filters_exclude:
- "*processed*"
extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
- "fastqc":
name: "Falco (pre-Trimming)"
name: "FastQC / Falco (post-Trimming)"
path_filters:
- "*_raw_falco_*_report.html"
- "*processed*"
path_filters_exclude:
- "*raw*"
extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
- "fastp"
- "adapterRemoval"
- "porechop":
extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
- "fastqc":
name: "FastQC (post-Trimming)"
path_filters:
- "*_processed_*fastqc.zip"
- "fastqc":
name: "Falco (post-Trimming)"
path_filters:
- "*_processed_falco_*_report.html"
- "bbduk"
- "prinseqplusplus"
- "filtlong"
@ -105,19 +107,20 @@ top_modules:
#It is not possible to set placement for custom kraken and centrifuge columns.
table_columns_placement:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: 100
avg_sequence_length: 110
median_sequence_length: 120
percent_duplicates: 130
percent_gc: 140
percent_fails: 150
Falco (pre-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: 200
avg_sequence_length: 210
percent_duplicates: 220
percent_gc: 230
percent_fails: 240
median_sequence_length: 220
percent_duplicates: 230
percent_gc: 240
percent_fails: 250
fastp:
pct_adapter: 300
pct_surviving: 310
@ -141,19 +144,6 @@ table_columns_placement:
Middle Split Percent: 460
Filtlong:
Target bases: 500
FastQC (post-Trimming):
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: 700
avg_sequence_length: 710
percent_duplicates: 720
percent_gc: 730
percent_fails: 740
BBDuk:
Input reads: 800
Total Removed bases percent: 810
@ -205,25 +195,18 @@ table_columns_placement:
"Number of ext-mOTUs": 1880
table_columns_visible:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_fails: False
Falco (pre-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: True
percent_gc: True
percent_duplicates: False
percent_gc: False
percent_fails: False
fastp:
pct_adapter: True
pct_surviving: True
pct_duplication: False
after_filtering_gc_content: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
porechop:
Input reads: False
Start Trimmed:
@ -232,6 +215,13 @@ table_columns_visible:
End Trimmed Percent: True
Middle Split: False
Middle Split Percent: True
fastp:
pct_adapter: True
pct_surviving: True
pct_duplication: False
after_filtering_gc_content: False
after_filtering_q30_rate: False
after_filtering_q30_bases: False
Filtlong:
Target bases: True
Adapter Removal:
@ -239,18 +229,6 @@ table_columns_visible:
percent_aligned: True
percent_collapsed: True
percent_discarded: False
FastQC (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
Falco (post-Trimming):
total_sequences: True
avg_sequence_length: True
percent_duplicates: False
percent_gc: False
percent_fails: False
BBDuk:
Input reads: False
Total Removed bases Percent: False
@ -278,25 +256,13 @@ table_columns_visible:
motus: False
table_columns_name:
FastQC (pre-Trimming):
FastQC / Falco (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
Falco (pre-Trimming):
total_sequences: "Nr. Input Reads"
avg_sequence_length: "Length Input Reads"
percent_gc: "% GC Input Reads"
percent_duplicates: "% Dups Input Reads"
percent_fails: "% Failed Input Reads"
FastQC (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
percent_duplicates: "% Dups Processed Reads"
percent_fails: "% Failed Processed Reads"
Falco (post-Trimming):
FastQC / Falco (post-Trimming):
total_sequences: "Nr. Processed Reads"
avg_sequence_length: "Length Processed Reads"
percent_gc: "% GC Processed Reads"
@ -314,7 +280,8 @@ extra_fn_clean_exts:
- ".bbduk"
- ".unmapped"
- "_filtered"
- "_processed"
- type: remove
pattern: "_falco"
section_comments:
general_stats: "By default, all read count columns are displayed as millions (M) of reads."

4
conf/modules.config
View file

@ -486,7 +486,7 @@ process {
ext.args = { "${meta.db_params}" }
}
withName: '.*PROFILING:KAIJU_KAIJU2TABLE' {
withName: 'KAIJU_KAIJU2TABLE_SINGLE' {
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
publishDir = [
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
@ -495,7 +495,7 @@ process {
]
}
withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' {
withName: 'KAIJU_KAIJU2TABLE_COMBINED' {
ext.prefix = { "kaiju_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/kaiju/" },

10
docs/output.md
View file

@ -35,19 +35,21 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
### FastQC or falco
### FastQC or Falco
<details markdown="1">
<summary>Output files</summary>
- `fastqc/`
- `*_fastqc.html`: FastQC report containing quality metrics.
- `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
- `*_fastqc.html`: FastQC or Falco report containing quality metrics.
- `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images (FastQC only).
</details>
[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
If preprocessing is turned on, nf-core/taxprofiler runs FastQC/Falco twice -once before and once after adapter removal/read merging, to allow evaluation of the performance of these preprocessing steps. Note in the General Stats table, the columns of these two instances of FastQC/Falco are placed next to each other to make it easier to evaluate. However, the columns of the actual preprocessing steps (i.e, fastp, AdapterRemoval, and Porechop) will be displayed _after_ the two FastQC/Falco columns, even if they were run 'between' the two FastQC/Falco jobs in the pipeline itself.
> ℹ️ Falco produces identical output to FastQC but in the `falco/` directory.
![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
@ -56,8 +58,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
### fastp
[fastp](https://github.com/OpenGene/fastp) is a FASTQ pre-processing tool for quality control, trimmming of adapters, quality filtering and other features.

34
subworkflows/local/profiling.nf
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@ -2,19 +2,19 @@
// Run profiling
//
include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_SINGLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
workflow PROFILING {
take:
@ -272,10 +272,10 @@ workflow PROFILING {
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_rank)
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
KAIJU_KAIJU2TABLE_SINGLE ( KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_rank)
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE_SINGLE.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE_SINGLE.out.summary )
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE_SINGLE.out.summary )
}
if ( params.run_diamond ) {

8
subworkflows/local/standardisation_profiles.nf
View file

@ -3,7 +3,7 @@
//
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KAIJU_KAIJU2TABLE as KAIJU_KAIJU2TABLE_COMBINED } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
@ -103,9 +103,9 @@ workflow STANDARDISATION_PROFILES {
[[id:it[0]], it[1]]
}
KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
KAIJU_KAIJU2TABLE_COMBINED ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE_COMBINED.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE_COMBINED.out.versions )
// Kraken2