mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:13:10 +00:00
update MultiQC and include latest modules
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parent
6dcf619518
commit
d6fa45b500
4 changed files with 94 additions and 45 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 +124,63 @@ 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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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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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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"Num. of queries": 1200
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Total reads: 1210
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Mappability: 1220
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Assig. Taxonomy: 1230
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Taxonomic assignment success: 1240
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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: 1300
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"% Assigned": 1310
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"% Unclassified": 1320
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table_columns_visible:
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FastQC (pre-Trimming):
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@ -176,6 +202,16 @@ 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 +229,14 @@ 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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@ -212,16 +256,19 @@ table_columns_visible:
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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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DIAMOND:
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queries_aligned: True
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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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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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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 +300,10 @@ 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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@ -300,7 +300,6 @@ 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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publishDir = [
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@ -173,7 +173,7 @@
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"installed_by": ["modules"]
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},
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"porechop/porechop": {
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6
modules/nf-core/multiqc/main.nf
generated
6
modules/nf-core/multiqc/main.nf
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process MULTIQC {
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label 'process_single'
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conda "bioconda::multiqc=1.13"
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conda "bioconda::multiqc=1.14"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
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'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
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input:
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path multiqc_files, stageAs: "?/*"
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