mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-11 00:23:08 +00:00
Merge branch 'nf-core:dev' into update_usage
This commit is contained in:
commit
502a4a81cd
16 changed files with 497 additions and 121 deletions
|
@ -19,11 +19,20 @@ custom_logo_title: "nf-core/taxprofiler"
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||||||
run_modules:
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run_modules:
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||||||
- fastqc
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- fastqc
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||||||
- adapterRemoval
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- adapterRemoval
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||||||
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- bbduk
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||||||
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- prinseqplusplus
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||||||
- fastp
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- fastp
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||||||
|
- filtlong
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||||||
- bowtie2
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- bowtie2
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||||||
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- minimap2
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||||||
- samtools
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- samtools
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||||||
- kraken
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- kraken
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||||||
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- kaiju
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||||||
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- metaphlan
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- diamond
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- malt
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- malt
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- motus
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- porechop
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||||||
- custom_content
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- custom_content
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||||||
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|
||||||
#extra_fn_clean_exts:
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#extra_fn_clean_exts:
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||||||
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@ -36,16 +45,41 @@ top_modules:
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||||||
name: "FastQC (pre-Trimming)"
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name: "FastQC (pre-Trimming)"
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||||||
path_filters:
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path_filters:
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||||||
- "*raw_*fastqc.zip"
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- "*raw_*fastqc.zip"
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||||||
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- "fastqc":
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||||||
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name: "Falco (pre-Trimming)"
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||||||
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path_filters:
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||||||
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- "*_raw_falco_*_report.html"
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||||||
- "fastp"
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- "fastp"
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||||||
- "adapterRemoval"
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- "adapterRemoval"
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||||||
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- "porechop"
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||||||
- "fastqc":
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- "fastqc":
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||||||
name: "FastQC (post-Trimming)"
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name: "FastQC (post-Trimming)"
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||||||
path_filters:
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path_filters:
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||||||
- "*raw_*processed.zip"
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- "*_processed_*fastqc.zip"
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||||||
|
- "fastqc":
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||||||
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name: "Falco (post-Trimming)"
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||||||
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path_filters:
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||||||
|
- "*_processed_falco_*_report.html"
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||||||
|
- "bbduk"
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||||||
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- "prinseqplusplus"
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||||||
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- "filtlong"
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||||||
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- "bowtie2":
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name: "bowtie2"
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- "samtools":
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name: "Samtools Stats"
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||||||
- "kraken":
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- "kraken":
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name: "Kraken"
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name: "Kraken"
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||||||
path_filters:
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path_filters:
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||||||
- "*.kraken2.report.txt"
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- "*.kraken2.kraken2.report.txt"
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||||||
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- "kraken":
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name: "Bracken"
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anchor: "bracken"
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target: "Bracken"
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doi: "10.7717/peerj-cs.104"
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info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
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extra: "Note: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
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path_filters:
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||||||
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- "*.bracken.kraken2.report.txt"
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- "kraken":
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- "kraken":
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name: "Centrifuge"
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name: "Centrifuge"
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anchor: "centrifuge"
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anchor: "centrifuge"
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@ -55,3 +89,171 @@ top_modules:
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||||||
extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
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extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
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||||||
path_filters:
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path_filters:
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||||||
- "*.centrifuge.txt"
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- "*.centrifuge.txt"
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||||||
|
- "malt":
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||||||
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name: "MALT"
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- "diamond"
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||||||
|
- "kaiju":
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||||||
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name: "Kaiju"
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||||||
|
- "motus"
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||||||
|
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||||||
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#It is not possible to set placement for custom kraken and centrifuge columns.
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|
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|
table_columns_placement:
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|
FastQC (pre-Trimming):
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||||||
|
total_sequences: 100
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||||||
|
avg_sequence_length: 110
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||||||
|
percent_duplicates: 120
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||||||
|
percent_gc: 130
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||||||
|
percent_fails: 140
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||||||
|
Falco (pre-Trimming):
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||||||
|
total_sequences: 200
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||||||
|
avg_sequence_length: 210
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||||||
|
percent_duplicates: 220
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||||||
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percent_gc: 230
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||||||
|
percent_fails: 240
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||||||
|
fastp:
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||||||
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pct_adapter: 300
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||||||
|
pct_surviving: 310
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||||||
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pct_duplication: 320
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||||||
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after_filtering_gc_content: 330
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||||||
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after_filtering_q30_rate: 340
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||||||
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after_filtering_q30_bases: 350
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||||||
|
Adapter Removal:
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||||||
|
aligned_total: 360
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||||||
|
percent_aligned: 370
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||||||
|
percent_collapsed: 380
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||||||
|
percent_discarded: 390
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||||||
|
FastQC (post-Trimming):
|
||||||
|
total_sequences: 400
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||||||
|
avg_sequence_length: 410
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||||||
|
percent_duplicates: 420
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||||||
|
percent_gc: 430
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||||||
|
percent_fails: 440
|
||||||
|
Falco (post-Trimming):
|
||||||
|
total_sequences: 500
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||||||
|
avg_sequence_length: 510
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||||||
|
percent_duplicates: 520
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||||||
|
percent_gc: 530
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||||||
|
percent_fails: 540
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||||||
|
bowtie2:
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||||||
|
overall_alignment_rate: 600
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||||||
|
Samtools Stats:
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||||||
|
raw_total_sequences: 700
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||||||
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reads_mapped: 710
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||||||
|
reads_mapped_percent: 720
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||||||
|
reads_properly_paired_percent: 730
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||||||
|
non-primary_alignments: 740
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||||||
|
reads_MQ0_percent: 750
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||||||
|
error_rate: 760
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||||||
|
MALT:
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||||||
|
Num. of queries: 1000
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||||||
|
Total reads: 1100
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||||||
|
Mappability: 1200
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||||||
|
Assig. Taxonomy: 1300
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||||||
|
Taxonomic assignment success: 1400
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||||||
|
Kaiju:
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||||||
|
assigned: 2000
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||||||
|
"% Assigned": 2100
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||||||
|
"% Unclassified": 2200
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||||||
|
|
||||||
|
table_columns_visible:
|
||||||
|
FastQC (pre-Trimming):
|
||||||
|
total_sequences: True
|
||||||
|
avg_sequence_length: True
|
||||||
|
percent_duplicates: True
|
||||||
|
percent_gc: True
|
||||||
|
percent_fails: False
|
||||||
|
Falco (pre-Trimming):
|
||||||
|
total_sequences: True
|
||||||
|
avg_sequence_length: True
|
||||||
|
percent_duplicates: True
|
||||||
|
percent_gc: True
|
||||||
|
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
|
||||||
|
Adapter Removal:
|
||||||
|
aligned_total: True
|
||||||
|
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
|
||||||
|
bowtie2:
|
||||||
|
overall_alignment_rate: True
|
||||||
|
Samtools Stats:
|
||||||
|
raw_total_sequences: True
|
||||||
|
reads_mapped: True
|
||||||
|
reads_mapped_percent: True
|
||||||
|
reads_properly_paired_percent: False
|
||||||
|
non-primary_alignments: False
|
||||||
|
reads_MQ0_percent: False
|
||||||
|
error_rate: False
|
||||||
|
Kraken:
|
||||||
|
"% Unclassified": True
|
||||||
|
"% Top 5": False
|
||||||
|
Bracken:
|
||||||
|
"% Unclassified": True
|
||||||
|
"% Top 5": False
|
||||||
|
Centrifuge:
|
||||||
|
"% Unclassified": True
|
||||||
|
"% Top 5": 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
|
||||||
|
table_columns_name:
|
||||||
|
FastQC (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):
|
||||||
|
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"
|
||||||
|
Samtools Stats:
|
||||||
|
raw_total_sequences: "Nr. Reads Into Mapping"
|
||||||
|
reads_mapped: "Nr. Mapped Reads"
|
||||||
|
reads_mapped_percent: "% Mapped Reads"
|
||||||
|
|
||||||
|
extra_fn_clean_exts:
|
||||||
|
- ".kraken2.kraken2.report.txt"
|
||||||
|
- ".centrifuge.txt"
|
||||||
|
- ".bracken.kraken2.report.txt"
|
||||||
|
- ".settings"
|
||||||
|
|
|
@ -12,14 +12,6 @@
|
||||||
|
|
||||||
process {
|
process {
|
||||||
|
|
||||||
withName: DATABASE_CHECK {
|
|
||||||
publishDir = [
|
|
||||||
path: { "${params.outdir}/pipeline_info" },
|
|
||||||
mode: params.publish_dir_mode,
|
|
||||||
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
|
|
||||||
]
|
|
||||||
}
|
|
||||||
|
|
||||||
withName: FASTQC {
|
withName: FASTQC {
|
||||||
ext.args = '--quiet'
|
ext.args = '--quiet'
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
|
||||||
|
@ -41,7 +33,7 @@ process {
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: FALCO {
|
withName: FALCO {
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/falco/raw" },
|
path: { "${params.outdir}/falco/raw" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
|
@ -50,7 +42,7 @@ process {
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: FALCO_PROCESSED {
|
withName: FALCO_PROCESSED {
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/falco/processed" },
|
path: { "${params.outdir}/falco/processed" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
|
@ -69,10 +61,17 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/fastp" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/fastp" },
|
||||||
pattern: '*.fastq.gz',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/fastp" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.{log,html,json}'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -90,10 +89,17 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/fastp" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/fastp" },
|
||||||
pattern: '*.fastq.gz',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/fastp" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.{log,html,json}'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -106,10 +112,17 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/adapterremoval" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/adapterremoval" },
|
||||||
pattern: '*.fastq.gz',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/adapterremoval" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.settings'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -125,20 +138,34 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/adapterremoval" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/adapterremoval" },
|
||||||
pattern: '*.fastq.gz',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/adapterremoval" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.settings'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: PORECHOP_PORECHOP {
|
withName: PORECHOP_PORECHOP {
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/porechop" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/porechop" },
|
||||||
pattern: '*.fastq.gz',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/porechop" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.log'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -151,10 +178,17 @@ process {
|
||||||
.join(' ').trim()
|
.join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/filtlong" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/filtlong" },
|
||||||
pattern: '*.{fastq.gz,log}',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_preprocessed_reads
|
pattern: '*.fastq.gz',
|
||||||
|
enabled: params.save_preprocessed_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/filtlong" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.log'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -171,21 +205,21 @@ process {
|
||||||
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
ext.prefix = { "${meta.id}_${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
[
|
[
|
||||||
path: { "${params.outdir}/bowtie2/align" },
|
path: { "${params.outdir}/bowtie2/align" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
pattern: '*.log'
|
pattern: '*.log'
|
||||||
],
|
],
|
||||||
[
|
[
|
||||||
path: { "${params.outdir}/bowtie2/align" },
|
path: { "${params.outdir}/bowtie2/align" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_hostremoval_mapped,
|
enabled: params.save_hostremoval_mapped,
|
||||||
pattern: '*.bam'
|
pattern: '*.bam'
|
||||||
],
|
],
|
||||||
[
|
[
|
||||||
path: { "${params.outdir}/bowtie2/align" },
|
path: { "${params.outdir}/bowtie2/align" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_hostremoval_unmapped,
|
enabled: params.save_hostremoval_unmapped,
|
||||||
pattern: '*.fastq.gz'
|
pattern: '*.fastq.gz'
|
||||||
]
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
@ -248,10 +282,17 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/bbduk/" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/bbduk/" },
|
||||||
pattern: '*.{fastq.gz,log}',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_complexityfiltered_reads
|
pattern: '*.{fastq.gz,log}',
|
||||||
|
enabled: params.save_complexityfiltered_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/bbduk/" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.log'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -263,10 +304,17 @@ process {
|
||||||
].join(' ').trim()
|
].join(' ').trim()
|
||||||
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
ext.prefix = { "${meta.id}-${meta.run_accession}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/prinseqplusplus/" },
|
[
|
||||||
mode: params.publish_dir_mode,
|
path: { "${params.outdir}/prinseqplusplus/" },
|
||||||
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
|
mode: params.publish_dir_mode,
|
||||||
enabled: params.save_complexityfiltered_reads
|
pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
|
||||||
|
enabled: params.save_complexityfiltered_reads
|
||||||
|
],
|
||||||
|
[
|
||||||
|
path: { "${params.outdir}/prinseqplusplus/" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.log'
|
||||||
|
]
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -303,7 +351,7 @@ process {
|
||||||
|
|
||||||
withName: KRAKEN2_KRAKEN2 {
|
withName: KRAKEN2_KRAKEN2 {
|
||||||
ext.args = params.kraken2_save_minimizers ? { "${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.id}-${meta.db_name}" } : { "${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}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||||
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,
|
||||||
|
@ -313,7 +361,7 @@ process {
|
||||||
|
|
||||||
withName: BRACKEN_BRACKEN {
|
withName: BRACKEN_BRACKEN {
|
||||||
errorStrategy = 'ignore'
|
errorStrategy = 'ignore'
|
||||||
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}-${meta.db_name}.bracken" } : { "${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,
|
||||||
|
@ -321,12 +369,21 @@ process {
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: KRAKENTOOLS_COMBINEKREPORTS {
|
withName: BRACKEN_COMBINEBRACKENOUTPUTS {
|
||||||
|
ext.prefix = { "bracken_${meta.id}_combined_reports" }
|
||||||
|
publishDir = [
|
||||||
|
path: { "${params.outdir}/bracken/" },
|
||||||
|
mode: params.publish_dir_mode,
|
||||||
|
pattern: '*.txt'
|
||||||
|
]
|
||||||
|
}
|
||||||
|
|
||||||
|
withName: KRAKENTOOLS_COMBINEKREPORTS_KRAKEN {
|
||||||
ext.prefix = { "kraken2_${meta.id}_combined_reports" }
|
ext.prefix = { "kraken2_${meta.id}_combined_reports" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
path: { "${params.outdir}/kraken2/" },
|
path: { "${params.outdir}/kraken2/" },
|
||||||
mode: params.publish_dir_mode,
|
mode: params.publish_dir_mode,
|
||||||
pattern: '*.{txt}'
|
pattern: '*.txt'
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
12
modules.json
12
modules.json
|
@ -30,6 +30,11 @@
|
||||||
"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
|
"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1",
|
||||||
"installed_by": ["modules"]
|
"installed_by": ["modules"]
|
||||||
},
|
},
|
||||||
|
"bracken/combinebrackenoutputs": {
|
||||||
|
"branch": "master",
|
||||||
|
"git_sha": "9c87d5fdad182590a370ea43a4ecebd200a6f6fb",
|
||||||
|
"installed_by": ["modules"]
|
||||||
|
},
|
||||||
"cat/fastq": {
|
"cat/fastq": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
|
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
|
||||||
|
@ -68,7 +73,8 @@
|
||||||
"falco": {
|
"falco": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
|
"git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
|
||||||
"installed_by": ["modules"]
|
"installed_by": ["modules"],
|
||||||
|
"patch": "modules/nf-core/falco/falco.diff"
|
||||||
},
|
},
|
||||||
"fastp": {
|
"fastp": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
|
@ -167,12 +173,12 @@
|
||||||
},
|
},
|
||||||
"motus/merge": {
|
"motus/merge": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
|
"git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
|
||||||
"installed_by": ["modules"]
|
"installed_by": ["modules"]
|
||||||
},
|
},
|
||||||
"motus/profile": {
|
"motus/profile": {
|
||||||
"branch": "master",
|
"branch": "master",
|
||||||
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
|
"git_sha": "3fce766123e71e82fb384db7d07b59180baa9ee9",
|
||||||
"installed_by": ["modules"]
|
"installed_by": ["modules"]
|
||||||
},
|
},
|
||||||
"multiqc": {
|
"multiqc": {
|
||||||
|
|
|
@ -1,29 +0,0 @@
|
||||||
process DATABASE_CHECK {
|
|
||||||
tag "$databasesheet"
|
|
||||||
label 'process_single'
|
|
||||||
|
|
||||||
conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
|
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
||||||
'https://depot.galaxyproject.org/singularity/python:3.8.3' :
|
|
||||||
'quay.io/biocontainers/python:3.8.3' }"
|
|
||||||
|
|
||||||
input:
|
|
||||||
path databasesheet
|
|
||||||
|
|
||||||
output:
|
|
||||||
path '*.csv' , emit: csv
|
|
||||||
path "versions.yml", emit: versions
|
|
||||||
|
|
||||||
when:
|
|
||||||
task.ext.when == null || task.ext.when
|
|
||||||
|
|
||||||
script: // This script is bundled with the pipeline, in nf-core/taxprofiler/bin/
|
|
||||||
"""
|
|
||||||
cat $databasesheet >> database_sheet.valid.csv
|
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
|
||||||
"${task.process}":
|
|
||||||
python: \$(python --version | sed 's/Python //g')
|
|
||||||
END_VERSIONS
|
|
||||||
"""
|
|
||||||
}
|
|
37
modules/nf-core/bracken/combinebrackenoutputs/main.nf
generated
Normal file
37
modules/nf-core/bracken/combinebrackenoutputs/main.nf
generated
Normal file
|
@ -0,0 +1,37 @@
|
||||||
|
process BRACKEN_COMBINEBRACKENOUTPUTS {
|
||||||
|
tag "$meta.id"
|
||||||
|
label 'process_low'
|
||||||
|
|
||||||
|
conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
|
||||||
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
|
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
|
||||||
|
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
|
||||||
|
|
||||||
|
input:
|
||||||
|
tuple val(meta), path(input)
|
||||||
|
|
||||||
|
output:
|
||||||
|
tuple val(meta), path("*.txt"), emit: txt
|
||||||
|
path "versions.yml" , emit: versions
|
||||||
|
|
||||||
|
when:
|
||||||
|
task.ext.when == null || task.ext.when
|
||||||
|
|
||||||
|
script:
|
||||||
|
def args = task.ext.args ?: ''
|
||||||
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||||||
|
// WARN: Version information not provided by tool on CLI.
|
||||||
|
// Please update version string below when bumping container versions.
|
||||||
|
def VERSION = '2.7'
|
||||||
|
"""
|
||||||
|
combine_bracken_outputs.py \\
|
||||||
|
$args \\
|
||||||
|
--files ${input} \\
|
||||||
|
-o ${prefix}.txt
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
combine_bracken_output: ${VERSION}
|
||||||
|
END_VERSIONS
|
||||||
|
"""
|
||||||
|
}
|
41
modules/nf-core/bracken/combinebrackenoutputs/meta.yml
generated
Normal file
41
modules/nf-core/bracken/combinebrackenoutputs/meta.yml
generated
Normal file
|
@ -0,0 +1,41 @@
|
||||||
|
name: "bracken_combinebrackenoutputs"
|
||||||
|
description: Combine output of metagenomic samples analyzed by bracken.
|
||||||
|
keywords:
|
||||||
|
- sort
|
||||||
|
tools:
|
||||||
|
- "bracken":
|
||||||
|
description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
|
||||||
|
homepage: https://ccb.jhu.edu/software/bracken/
|
||||||
|
documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
|
||||||
|
tool_dev_url: https://github.com/jenniferlu717/Bracken
|
||||||
|
doi: "10.7717/peerj-cs.104"
|
||||||
|
licence: ["GPL v3"]
|
||||||
|
|
||||||
|
input:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- input:
|
||||||
|
type: file
|
||||||
|
description: List of output files from bracken
|
||||||
|
pattern: "*"
|
||||||
|
|
||||||
|
output:
|
||||||
|
- meta:
|
||||||
|
type: map
|
||||||
|
description: |
|
||||||
|
Groovy Map containing sample information
|
||||||
|
e.g. [ id:'test', single_end:false ]
|
||||||
|
- versions:
|
||||||
|
type: file
|
||||||
|
description: File containing software versions
|
||||||
|
pattern: "versions.yml"
|
||||||
|
- txt:
|
||||||
|
type: file
|
||||||
|
description: Combined output in table format
|
||||||
|
pattern: "*.txt"
|
||||||
|
|
||||||
|
authors:
|
||||||
|
- "@jfy133"
|
16
modules/nf-core/falco/falco.diff
generated
Normal file
16
modules/nf-core/falco/falco.diff
generated
Normal file
|
@ -0,0 +1,16 @@
|
||||||
|
Changes in module 'nf-core/falco'
|
||||||
|
--- modules/nf-core/falco/main.nf
|
||||||
|
+++ modules/nf-core/falco/main.nf
|
||||||
|
@@ -33,7 +33,9 @@
|
||||||
|
"""
|
||||||
|
} else {
|
||||||
|
"""
|
||||||
|
- falco $args --threads $task.cpus ${reads}
|
||||||
|
+ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||||
|
+ [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||||
|
+ falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||||
|
|
||||||
|
cat <<-END_VERSIONS > versions.yml
|
||||||
|
"${task.process}":
|
||||||
|
|
||||||
|
************************************************************
|
4
modules/nf-core/falco/main.nf
generated
4
modules/nf-core/falco/main.nf
generated
|
@ -33,7 +33,9 @@ process FALCO {
|
||||||
"""
|
"""
|
||||||
} else {
|
} else {
|
||||||
"""
|
"""
|
||||||
falco $args --threads $task.cpus ${reads}
|
[ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
|
||||||
|
[ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
|
||||||
|
falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
|
||||||
|
|
||||||
cat <<-END_VERSIONS > versions.yml
|
cat <<-END_VERSIONS > versions.yml
|
||||||
"${task.process}":
|
"${task.process}":
|
||||||
|
|
8
modules/nf-core/motus/merge/main.nf
generated
8
modules/nf-core/motus/merge/main.nf
generated
|
@ -1,13 +1,11 @@
|
||||||
VERSION = '3.0.1'
|
|
||||||
|
|
||||||
process MOTUS_MERGE {
|
process MOTUS_MERGE {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_single'
|
label 'process_single'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
|
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
|
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
|
||||||
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
|
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(input)
|
tuple val(meta), path(input)
|
||||||
|
|
2
modules/nf-core/motus/merge/meta.yml
generated
2
modules/nf-core/motus/merge/meta.yml
generated
|
@ -14,7 +14,7 @@ tools:
|
||||||
homepage: "https://motu-tool.org/"
|
homepage: "https://motu-tool.org/"
|
||||||
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
||||||
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
||||||
doi: "10.1038/s41467-019-08844-4"
|
doi: "10.1186/s40168-022-01410-z"
|
||||||
licence: "['GPL v3']"
|
licence: "['GPL v3']"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
|
6
modules/nf-core/motus/profile/main.nf
generated
6
modules/nf-core/motus/profile/main.nf
generated
|
@ -2,10 +2,10 @@ process MOTUS_PROFILE {
|
||||||
tag "$meta.id"
|
tag "$meta.id"
|
||||||
label 'process_medium'
|
label 'process_medium'
|
||||||
|
|
||||||
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
|
conda (params.enable_conda ? "bioconda::motus=3.0.3" : null)
|
||||||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||||
'https://depot.galaxyproject.org/singularity/motus:3.0.1--pyhdfd78af_0':
|
'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0':
|
||||||
'quay.io/biocontainers/motus:3.0.1--pyhdfd78af_0' }"
|
'quay.io/biocontainers/motus:3.0.3--pyhdfd78af_0' }"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
tuple val(meta), path(reads)
|
tuple val(meta), path(reads)
|
||||||
|
|
2
modules/nf-core/motus/profile/meta.yml
generated
2
modules/nf-core/motus/profile/meta.yml
generated
|
@ -11,7 +11,7 @@ tools:
|
||||||
homepage: "https://motu-tool.org/"
|
homepage: "https://motu-tool.org/"
|
||||||
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
documentation: "https://github.com/motu-tool/mOTUs/wiki"
|
||||||
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
tool_dev_url: "https://github.com/motu-tool/mOTUs"
|
||||||
doi: "10.1038/s41467-019-08844-4"
|
doi: "10.1186/s40168-022-01410-z"
|
||||||
licence: "['GPL v3']"
|
licence: "['GPL v3']"
|
||||||
|
|
||||||
input:
|
input:
|
||||||
|
|
|
@ -2,7 +2,6 @@
|
||||||
// Check input samplesheet and get read channels
|
// Check input samplesheet and get read channels
|
||||||
//
|
//
|
||||||
|
|
||||||
include { DATABASE_CHECK } from '../../modules/local/database_check'
|
|
||||||
include { UNTAR } from '../../modules/nf-core/untar/main'
|
include { UNTAR } from '../../modules/nf-core/untar/main'
|
||||||
|
|
||||||
workflow DB_CHECK {
|
workflow DB_CHECK {
|
||||||
|
@ -10,15 +9,27 @@ workflow DB_CHECK {
|
||||||
dbsheet // file: /path/to/dbsheet.csv
|
dbsheet // file: /path/to/dbsheet.csv
|
||||||
|
|
||||||
main:
|
main:
|
||||||
|
ch_versions = Channel.empty()
|
||||||
|
|
||||||
// TODO: make database sheet check
|
// special check to check _between_ rows, for which we must group rows together
|
||||||
// Checks:
|
// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
|
||||||
// 1) no duplicates,
|
Channel.fromPath(dbsheet)
|
||||||
// 2) args do not have quotes, e.g. just `,,` and NOT `,"",`
|
.splitCsv ( header:true, sep:',' )
|
||||||
parsed_samplesheet = DATABASE_CHECK ( dbsheet )
|
.map {[it.tool, it.db_name] }
|
||||||
.csv
|
.groupTuple()
|
||||||
|
.map {
|
||||||
|
tool, db_name ->
|
||||||
|
def unique_names = db_name.unique(false)
|
||||||
|
if ( unique_names.size() < db_name.size() ) exit 1, "[nf-core/taxprofiler] ERROR: Each database for a tool must have a unique name, duplicated detected. Tool: ${tool}, Database name: ${unique_names}"
|
||||||
|
}
|
||||||
|
|
||||||
|
// normal checks for within-row validity, so can be moved to separate functions
|
||||||
|
parsed_samplesheet = Channel.fromPath(dbsheet)
|
||||||
.splitCsv ( header:true, sep:',' )
|
.splitCsv ( header:true, sep:',' )
|
||||||
.map { create_db_channels(it) }
|
.map {
|
||||||
|
validate_db_rows(it)
|
||||||
|
create_db_channels(it)
|
||||||
|
}
|
||||||
|
|
||||||
ch_dbs_for_untar = parsed_samplesheet
|
ch_dbs_for_untar = parsed_samplesheet
|
||||||
.branch {
|
.branch {
|
||||||
|
@ -29,12 +40,32 @@ workflow DB_CHECK {
|
||||||
// TODO Filter to only run UNTAR on DBs of tools actually using?
|
// TODO Filter to only run UNTAR on DBs of tools actually using?
|
||||||
// TODO make optional whether to save
|
// TODO make optional whether to save
|
||||||
UNTAR ( ch_dbs_for_untar.untar )
|
UNTAR ( ch_dbs_for_untar.untar )
|
||||||
|
ch_versions = ch_versions.mix(UNTAR.out.versions.first())
|
||||||
|
|
||||||
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
|
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
|
||||||
|
|
||||||
emit:
|
emit:
|
||||||
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
|
dbs = ch_final_dbs // channel: [ val(meta), [ db ] ]
|
||||||
versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ]
|
versions = ch_versions // channel: [ versions.yml ]
|
||||||
|
}
|
||||||
|
|
||||||
|
def validate_db_rows(LinkedHashMap row){
|
||||||
|
|
||||||
|
// check minimum number of columns
|
||||||
|
if (row.size() < 4) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed row (e.g. missing column). See documentation for more information. Error in: ${row}"
|
||||||
|
|
||||||
|
// all columns there
|
||||||
|
def expected_headers = ['tool', 'db_name', 'db_params', 'db_path']
|
||||||
|
if ( !row.keySet().containsAll(expected_headers) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database input sheet - malformed column names. Please check input TSV. Column names should be: ${expected_keys.join(", ")}"
|
||||||
|
|
||||||
|
// valid tools specified// TIFNISIH LIST
|
||||||
|
def expected_tools = [ "bracken", "centrifuge", "diamond", "kaiju", "kraken2", "krakenuniq", "malt", "metaphlan3", "motus" ]
|
||||||
|
if ( !expected_tools.contains(row.tool) ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid tool name. Please see documentation for all supported profilers. Error in: ${row}"
|
||||||
|
|
||||||
|
// detect quotes in params
|
||||||
|
if ( row.db_params.contains('"') ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||||
|
if ( row.db_params.contains("'") ) exit 1, "[nf-core/taxprofiler] ERROR: Invalid database db_params entry. No quotes allowed. Error in: ${row}"
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
def create_db_channels(LinkedHashMap row) {
|
def create_db_channels(LinkedHashMap row) {
|
||||||
|
@ -45,9 +76,11 @@ def create_db_channels(LinkedHashMap row) {
|
||||||
|
|
||||||
def array = []
|
def array = []
|
||||||
if (!file(row.db_path, type: 'dir').exists()) {
|
if (!file(row.db_path, type: 'dir').exists()) {
|
||||||
exit 1, "ERROR: Please check input samplesheet -> database could not be found!\n${row.db_path}"
|
exit 1, "ERROR: Please check input samplesheet -> database path could not be found!\n${row.db_path}"
|
||||||
}
|
}
|
||||||
array = [ meta, file(row.db_path) ]
|
array = [ meta, file(row.db_path) ]
|
||||||
|
|
||||||
return array
|
return array
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
|
@ -41,14 +41,14 @@ workflow PROFILING {
|
||||||
}
|
}
|
||||||
.combine(databases)
|
.combine(databases)
|
||||||
.branch {
|
.branch {
|
||||||
malt: it[2]['tool'] == 'malt'
|
|
||||||
kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
|
|
||||||
metaphlan3: it[2]['tool'] == 'metaphlan3'
|
|
||||||
centrifuge: it[2]['tool'] == 'centrifuge'
|
centrifuge: it[2]['tool'] == 'centrifuge'
|
||||||
kaiju: it[2]['tool'] == 'kaiju'
|
|
||||||
diamond: it[2]['tool'] == 'diamond'
|
diamond: it[2]['tool'] == 'diamond'
|
||||||
motus: it[2]['tool'] == 'motus'
|
kaiju: it[2]['tool'] == 'kaiju'
|
||||||
|
kraken2: it[2]['tool'] == 'kraken2' || it[2]['tool'] == 'bracken' // to reuse the kraken module to produce the input data for bracken
|
||||||
krakenuniq: it[2]['tool'] == 'krakenuniq'
|
krakenuniq: it[2]['tool'] == 'krakenuniq'
|
||||||
|
malt: it[2]['tool'] == 'malt'
|
||||||
|
metaphlan3: it[2]['tool'] == 'metaphlan3'
|
||||||
|
motus: it[2]['tool'] == 'motus'
|
||||||
unknown: true
|
unknown: true
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -2,6 +2,7 @@
|
||||||
// Standardise output files e.g. aggregation
|
// Standardise output files e.g. aggregation
|
||||||
//
|
//
|
||||||
|
|
||||||
|
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
|
||||||
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
|
include { KAIJU_KAIJU2TABLE } 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_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
|
||||||
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
|
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
|
||||||
|
@ -25,10 +26,11 @@ workflow STANDARDISATION_PROFILES {
|
||||||
*/
|
*/
|
||||||
ch_input_profiles = profiles
|
ch_input_profiles = profiles
|
||||||
.branch {
|
.branch {
|
||||||
motus: it[0]['tool'] == 'motus'
|
bracken: it[0]['tool'] == 'bracken'
|
||||||
kraken2: it[0]['tool'] == 'kraken2'
|
|
||||||
centrifuge: it[0]['tool'] == 'centrifuge'
|
centrifuge: it[0]['tool'] == 'centrifuge'
|
||||||
|
kraken2: it[0]['tool'] == 'kraken2'
|
||||||
metaphlan3: it[0]['tool'] == 'metaphlan3'
|
metaphlan3: it[0]['tool'] == 'metaphlan3'
|
||||||
|
motus: it[0]['tool'] == 'motus'
|
||||||
unknown: true
|
unknown: true
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -49,7 +51,18 @@ workflow STANDARDISATION_PROFILES {
|
||||||
Standardise and aggregate
|
Standardise and aggregate
|
||||||
*/
|
*/
|
||||||
|
|
||||||
// CENTRIFUGE
|
// Bracken
|
||||||
|
|
||||||
|
ch_profiles_for_bracken = ch_input_profiles.bracken
|
||||||
|
.map { [it[0]['db_name'], it[1]] }
|
||||||
|
.groupTuple()
|
||||||
|
.map {
|
||||||
|
[[id:it[0]], it[1]]
|
||||||
|
}
|
||||||
|
|
||||||
|
BRACKEN_COMBINEBRACKENOUTPUTS ( ch_profiles_for_bracken )
|
||||||
|
|
||||||
|
// CENTRIFUGE
|
||||||
|
|
||||||
// Collect and replace id for db_name for prefix
|
// Collect and replace id for db_name for prefix
|
||||||
// Have to sort by size to ensure first file actually has hits otherwise
|
// Have to sort by size to ensure first file actually has hits otherwise
|
||||||
|
|
|
@ -25,7 +25,7 @@ if ( params.input ) {
|
||||||
exit 1, "Input samplesheet, or PEP config and base directory not specified"
|
exit 1, "Input samplesheet, or PEP config and base directory not specified"
|
||||||
}
|
}
|
||||||
|
|
||||||
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
|
if (params.databases) { ch_databases = file(params.databases, checkIfExists: true) } else { exit 1, 'Input database sheet not specified!' }
|
||||||
|
|
||||||
if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
|
if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
|
||||||
if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
|
if (params.shortread_qc_includeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging is not turned on. Please specify --shortread_qc_mergepairs"
|
||||||
|
|
Loading…
Reference in a new issue