mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 08:49:55 +00:00
Merge branch 'nf-core:dev' into update_output
This commit is contained in:
Sofia Stamouli
GitHub
commit
244fe5e30d
4 changed files with 148 additions and 67 deletions
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@ -19,9 +19,10 @@ custom_logo_title: "nf-core/taxprofiler"
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run_modules:
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- fastqc
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- adapterRemoval
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- fastp
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- bbduk
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- prinseqplusplus
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- fastp
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- porechop
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- filtlong
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- bowtie2
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- minimap2
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@ -32,9 +33,13 @@ run_modules:
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- diamond
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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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sp:
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diamond:
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contents: "diamond v"
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num_lines: 10
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#extra_fn_clean_exts:
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# - '_fastp'
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# - '.pe.settings'
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@ -102,9 +107,10 @@ 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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median_sequence_length: 120
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percent_duplicates: 130
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percent_gc: 140
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percent_fails: 150
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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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@ -118,43 +124,84 @@ table_columns_placement:
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after_filtering_gc_content: 330
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after_filtering_q30_rate: 340
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after_filtering_q30_bases: 350
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filtering_result_passed_filter_reads: 360
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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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Porechop:
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Input Reads: 400
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Start Trimmed: 410
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Start Trimmed Percent: 420
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End Trimmed: 430
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End Trimmed Percent: 440
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Middle Split: 450
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Middle Split Percent: 460
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Filtlong:
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Target bases: 500
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FastQC (post-Trimming):
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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
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total_sequences: 600
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avg_sequence_length: 610
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median_sequence_length: 620
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percent_duplicates: 630
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percent_gc: 640
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percent_fails: 650
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Falco (post-Trimming):
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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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total_sequences: 700
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avg_sequence_length: 710
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percent_duplicates: 720
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percent_gc: 730
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percent_fails: 740
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BBDuk:
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Input reads: 800
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Total Removed bases percent: 810
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Total Removed bases: 820
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Total Removed reads percent: 830
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Total Removed reads: 840
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PRINSEQ++:
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prinseqplusplus_total: 900
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bowtie2:
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overall_alignment_rate: 600
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overall_alignment_rate: 1000
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Samtools Stats:
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raw_total_sequences: 700
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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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raw_total_sequences: 1100
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reads_mapped: 1110
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reads_mapped_percent: 1120
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reads_properly_paired_percent: 1130
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non-primary_alignments: 1140
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reads_MQ0_percent: 1150
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error_rate: 1160
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Bracken:
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"% Unclassified": 1200
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"% Top 5": 1210
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Centrifuge:
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"% Unclassified": 1300
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"% Top 5": 1310
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DIAMOND:
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queries_aligned: 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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assigned: 1500
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"% Assigned": 1510
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"% Unclassified": 1520
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Kraken:
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"% Unclassified": 1600
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"% Top 5": 1610
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MALT:
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"Num. of queries": 1700
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Total reads: 1710
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Mappability: 1720
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Assig. Taxonomy: 1730
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Taxonomic assignment success: 1740
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motus:
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Total number of reads: 1800
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Number of reads after filtering: 1810
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Total number of inserts: 1820
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Unique mappers: 1830
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Multiple mappers: 1840
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Ignored multiple mapper without unique hit: 1850
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"Number of ref-mOTUs": 1860
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"Number of meta-mOTUs": 1870
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"Number of ext-mOTUs": 1880
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table_columns_visible:
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FastQC (pre-Trimming):
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@ -176,6 +223,16 @@ table_columns_visible:
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after_filtering_gc_content: False
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after_filtering_q30_rate: False
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after_filtering_q30_bases: False
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porechop:
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Input reads: False
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Start Trimmed:
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Start Trimmed Percent: True
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End Trimmed: False
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End Trimmed Percent: True
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Middle Split: False
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Middle Split Percent: True
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Filtlong:
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Target bases: True
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Adapter Removal:
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aligned_total: True
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percent_aligned: True
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@ -193,6 +250,14 @@ table_columns_visible:
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percent_duplicates: False
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percent_gc: False
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percent_fails: False
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BBDuk:
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Input reads: False
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Total Removed bases Percent: False
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Total Removed bases: False
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Total Removed reads percent: True
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Total Removed reads: False
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"PRINSEQ++":
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prinseqplusplus_total: True
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bowtie2:
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overall_alignment_rate: True
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Samtools Stats:
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@ -204,24 +269,35 @@ table_columns_visible:
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reads_MQ0_percent: False
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error_rate: False
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Kraken:
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"% Unclassified": True
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"% Unclassified": False
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"% Top 5": False
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Bracken:
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"% Unclassified": True
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"% Unclassified": False
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"% Top 5": False
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Centrifuge:
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"% Unclassified": True
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"% Top 5": False
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MALT:
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Num. of queries: True
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Total reads: True
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Mappability: True
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Assig. Taxonomy: False
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Taxonomic assignment success: True
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Centrifuge: False
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DIAMOND:
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queries_aligned: False
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Kaiju:
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assigned: False
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"% Assigned": False
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"% Unclassified": True
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"% Unclassified": False
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MALT:
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"Num. of queries": False
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Total reads: False
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Mappability: False
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Assig. Taxonomy: False
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Taxonomic assignment success: False
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motus:
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Total number of reads: False
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Number of reads after filtering: False
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Total number of inserts: False
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Unique mappers: False
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Multiple mappers: False
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Ignored multiple mapper without unique hit: False
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"Number of ref-mOTUs": False
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"Number of meta-mOTUs": False
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"Number of ext-mOTUs": False
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table_columns_name:
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FastQC (pre-Trimming):
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total_sequences: "Nr. Input Reads"
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@ -253,7 +329,13 @@ table_columns_name:
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reads_mapped_percent: "% Mapped Reads"
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extra_fn_clean_exts:
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- ".kraken2.kraken2.report.txt"
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- ".centrifuge.txt"
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- ".bracken.kraken2.report.txt"
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- "kraken2.report.txt"
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- ".txt"
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- ".settings"
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- ".bbduk"
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- ".unmapped"
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- "_filtered"
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- "_processed"
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section_comments:
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general_stats: "By default, all read count columns are displayed as millions (M) of reads."
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@ -280,7 +280,7 @@ process {
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"entropywindow=${params.shortread_complexityfilter_bbduk_windowsize}",
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params.shortread_complexityfilter_bbduk_mask ? "entropymask=t" : "entropymask=f"
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/bbduk/" },
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@ -300,9 +300,8 @@ process {
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ext.args = [
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params.shortread_complexityfilter_prinseqplusplus_mode == 'dust' ? "-lc_dust=${params.shortread_complexityfilter_prinseqplusplus_dustscore}" : "-lc_entropy=${params.shortread_complexityfilter_entropy}",
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"-trim_qual_left=0 -trim_qual_left=0 -trim_qual_window=0 -trim_qual_step=0",
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"-VERBOSE 2"
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].join(' ').trim()
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ext.prefix = { "${meta.id}-${meta.run_accession}" }
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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[
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path: { "${params.outdir}/prinseqplusplus/" },
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@ -351,7 +350,7 @@ process {
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withName: KRAKEN2_KRAKEN2 {
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ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${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}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${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}_${meta.db_name}.kraken" }
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publishDir = [
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path: { "${params.outdir}/kraken2/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -361,7 +360,7 @@ process {
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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path: { "${params.outdir}/bracken/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -390,7 +389,7 @@ process {
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withName: KRAKENUNIQ_PRELOADEDKRAKENUNIQ {
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ext.args = { "${meta.db_params}" }
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// one run with multiple samples, so fix ID to just db name to ensure clean log name
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ext.prefix = { "${meta.db_name}" }
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ext.prefix = { "${meta.db_name}.krakenuniq" }
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publishDir = [
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path: { "${params.outdir}/krakenuniq/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -399,7 +398,7 @@ process {
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}
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withName: KRONA_CLEANUP {
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}" }
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publishDir = [
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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@ -408,7 +407,7 @@ process {
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}
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withName: KRONA_KTIMPORTTEXT {
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ext.prefix = { "${meta.tool}-${meta.id}" }
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ext.prefix = { "${meta.tool}_${meta.id}" }
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publishDir = [
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path: { "${params.outdir}/krona/" },
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mode: params.publish_dir_mode,
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@ -418,12 +417,12 @@ process {
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withName: 'MEGAN_RMA2INFO_KRONA' {
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ext.args = { "--read2class Taxonomy" }
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ext.prefix = { "${meta.id}-${meta.db_name}" }
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ext.prefix = { "${meta.id}_${meta.db_name}" }
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}
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withName: KRONA_KTIMPORTTAXONOMY {
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ext.args = "-i"
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ext.prefix = { "${meta.tool}-${meta.id}" }
|
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ext.prefix = { "${meta.tool}_${meta.id}" }
|
||||
publishDir = [
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path: { "${params.outdir}/krona/" },
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||||
mode: params.publish_dir_mode,
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@ -433,7 +432,7 @@ process {
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withName: METAPHLAN3_METAPHLAN3 {
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.metaphlan3" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.metaphlan3" }
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publishDir = [
|
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path: { "${params.outdir}/metaphlan3/${meta.db_name}/" },
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mode: params.publish_dir_mode,
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@ -457,13 +456,13 @@ process {
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pattern: '*.{txt,sam,gz}'
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]
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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" }
|
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.centrifuge" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.centrifuge" }
|
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}
|
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|
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withName: CENTRIFUGE_KREPORT {
|
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errorStrategy = {task.exitStatus == 255 ? 'ignore' : 'retry'}
|
||||
ext.args = { "${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/${meta.db_name}/" },
|
||||
mode: params.publish_dir_mode
|
||||
|
|
|
|||
|
|
@ -173,7 +173,7 @@
|
|||
},
|
||||
"multiqc": {
|
||||
"branch": "master",
|
||||
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
|
||||
"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
|
||||
"installed_by": ["modules"]
|
||||
},
|
||||
"porechop/porechop": {
|
||||
|
|
|
|||
6
modules/nf-core/multiqc/main.nf
generated
6
modules/nf-core/multiqc/main.nf
generated
|
|
@ -1,10 +1,10 @@
|
|||
process MULTIQC {
|
||||
label 'process_single'
|
||||
|
||||
conda "bioconda::multiqc=1.13"
|
||||
conda "bioconda::multiqc=1.14"
|
||||
container "${ 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: "?/*"
|
||||
|
|
|
|||
Loading…
Reference in a new issue