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Collapse FALCO and FASTQC sections, move FALCO/FASTQC sections together
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1 changed files with 27 additions and 76 deletions
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@ -51,37 +51,23 @@ sp:
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top_modules:
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- "fastqc":
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name: "FastQC (pre-Trimming)"
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name: "FastQC / Falco (pre-Trimming)"
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path_filters:
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- "*raw*"
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path_filters_exclude:
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- "*falco*"
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- "*processed*"
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extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
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- "fastqc":
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name: "Falco (pre-Trimming)"
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name: "FastQC / Falco (post-Trimming)"
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path_filters:
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- "*raw*"
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- "*[falco]*"
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path_filters_exclude:
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- "*processed*"
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path_filters_exclude:
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- "*raw*"
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extra: "If used in this run, Falco is a drop-in replacement for FastQC producing the same output, written by Guilherme de Sena Brandine and Andrew D. Smith."
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- "fastp"
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- "adapterRemoval"
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- "porechop":
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extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' this means that porechop did not detect any adapters and therefore no statistics generated."
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- "fastqc":
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name: "FastQC (post-Trimming)"
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path_filters:
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- "*processed*"
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path_filters_exclude:
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- "*falco*"
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- "*raw*"
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- "fastqc":
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name: "Falco (post-Trimming)"
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path_filters:
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- "*processed*"
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- "*falco*"
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path_filters_exclude:
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- "*raw*"
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- "bbduk"
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- "prinseqplusplus"
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- "filtlong"
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@ -121,19 +107,20 @@ top_modules:
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#It is not possible to set placement for custom kraken and centrifuge columns.
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table_columns_placement:
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FastQC (pre-Trimming):
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FastQC / Falco (pre-Trimming):
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total_sequences: 100
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avg_sequence_length: 110
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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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FastQC / Falco (post-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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percent_gc: 230
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percent_fails: 240
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median_sequence_length: 220
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percent_duplicates: 230
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percent_gc: 240
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percent_fails: 250
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fastp:
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pct_adapter: 300
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pct_surviving: 310
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@ -157,19 +144,6 @@ table_columns_placement:
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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: 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: 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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@ -221,25 +195,18 @@ table_columns_placement:
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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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FastQC / Falco (pre-Trimming):
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total_sequences: True
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avg_sequence_length: True
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percent_duplicates: True
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percent_gc: True
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percent_fails: False
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Falco (pre-Trimming):
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FastQC / Falco (post-Trimming):
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total_sequences: True
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avg_sequence_length: True
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percent_duplicates: True
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percent_gc: True
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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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fastp:
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pct_adapter: True
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pct_surviving: True
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pct_duplication: False
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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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@ -248,6 +215,13 @@ table_columns_visible:
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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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fastp:
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pct_adapter: True
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pct_surviving: True
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pct_duplication: False
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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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Filtlong:
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Target bases: True
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Adapter Removal:
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@ -255,18 +229,6 @@ table_columns_visible:
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percent_aligned: True
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percent_collapsed: True
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percent_discarded: False
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FastQC (post-Trimming):
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total_sequences: True
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avg_sequence_length: True
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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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Falco (post-Trimming):
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total_sequences: True
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avg_sequence_length: True
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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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@ -294,25 +256,13 @@ table_columns_visible:
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motus: False
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table_columns_name:
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FastQC (pre-Trimming):
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FastQC / Falco (pre-Trimming):
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total_sequences: "Nr. Input Reads"
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avg_sequence_length: "Length Input Reads"
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percent_gc: "% GC Input Reads"
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percent_duplicates: "% Dups Input Reads"
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percent_fails: "% Failed Input Reads"
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Falco (pre-Trimming):
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total_sequences: "Nr. Input Reads"
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avg_sequence_length: "Length Input Reads"
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percent_gc: "% GC Input Reads"
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percent_duplicates: "% Dups Input Reads"
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percent_fails: "% Failed Input Reads"
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FastQC (post-Trimming):
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total_sequences: "Nr. Processed Reads"
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avg_sequence_length: "Length Processed Reads"
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percent_gc: "% GC Processed Reads"
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percent_duplicates: "% Dups Processed Reads"
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percent_fails: "% Failed Processed Reads"
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Falco (post-Trimming):
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FastQC / Falco (post-Trimming):
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total_sequences: "Nr. Processed Reads"
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avg_sequence_length: "Length Processed Reads"
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percent_gc: "% GC Processed Reads"
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@ -330,7 +280,8 @@ extra_fn_clean_exts:
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- ".bbduk"
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- ".unmapped"
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- "_filtered"
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- "_processed"
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- type: remove
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pattern: "_falco"
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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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