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i/o handling
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@dorien-er
dorien-er committed Feb 27, 2024
1 parent e8a73f6 commit b71d715
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Showing 126 changed files with 15,880 additions and 36 deletions.
58 changes: 33 additions & 25 deletions src/multiqc/config.vsh.yaml
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Expand Up @@ -120,65 +120,73 @@ functionality:
example: path/to/multiqc_config.yml
description: |
Specific config file to load, after those in MultiQC dir / home dir / working dir
- name: "--profile_runtime"
type: boolean_true
description: |
Add analysis of how long MultiQC takes to run to the report
- name: "MultiQC behaviour"
arguments:
- name: "--verbose"
type: boolean_true
description: Increase output verbosity.
- name: "--force"
type: boolean_true
description: Overwrite any existing reports
description: |
Increase output verbosity.
- name: "--quiet"
type: boolean_true
description: Only show log warnings
description: |
Only show log warnings
- name: "--strict"
type: boolean_true
description: Don't catch exceptions, run additional code checks to help development.
description: |
Don't catch exceptions, run additional code checks to help development.
- name: "--development"
type: boolean_true
description: Development mode. Do not compress and minimise JS, export uncompressed plot data.
description: |
Development mode. Do not compress and minimise JS, export uncompressed plot data.
- name: "--require_logs"
type: boolean_true
description: Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.
description: |
Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.
- name: "--no_megaqc_upload"
type: boolean_true
description: Don't upload generated report to MegaQC, even if MegaQC options are found.
description: |
Don't upload generated report to MegaQC, even if MegaQC options are found.
- name: "--no_ansi"
type: boolean_true
description: Disable coloured log output.
description: |
Disable coloured log output.
- name: "Output format"
arguments:
- name: "--flat"
type: boolean_true
description: Use only flat plots (static images).
description: |
Use only flat plots (static images).
- name: "--interactive"
type: boolean_true
description: Use only interactive plots (in-browser Javascript).
- name: "--export"
type: boolean_true
description: Export plots as static images in addition to the report.
description: |
Use only interactive plots (in-browser Javascript).
- name: "--data_dir"
type: boolean_true
description: Force the parsed data directory to be created.
description: |
Force the parsed data directory to be created.
- name: "--no_data_dir"
type: boolean_true
description: Prevent the parsed data directory from being created.
description: |
Prevent the parsed data directory from being created.
- name: "--zip_data_dir"
type: boolean_true
description: Compress the data directory.
description: |
Compress the data directory.
- name: "--data_format"
type: string
choices: [tsv, csv, json, yaml]
description: Output parsed data in a different format.
- name: "--no_report"
type: boolean_true
description: Do not generate a report, only export data and plots.
description: |
Output parsed data in a different format than the default 'txt'.
- name: "--pdf"
type: boolean_true
description: Creates PDF report with the 'simple' template. Requires Pandoc to be installed.
description: |
Creates PDF report with the 'simple' template. Requires Pandoc to be installed.
resources:
- type: bash_script
Expand All @@ -192,7 +200,7 @@ functionality:

platforms:
- type: docker
image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_0
image: quay.io/biocontainers/multiqc:1.20--pyhdfd78af_2
setup:
- type: docker
run: |
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155 changes: 155 additions & 0 deletions src/multiqc/rna-seq/data/SRR3192396_1.fastq.gz_trimming_report.txt
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SUMMARISING RUN PARAMETERS
==========================
Input filename: SRR3192396_1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed


This is cutadapt 1.9.1 with Python 2.7.6
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR3192396_1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 2200.70 s (21 us/read; 2.87 M reads/minute).

=== Summary ===

Total reads processed: 105,089,150
Reads with adapters: 31,907,642 (30.4%)
Reads written (passing filters): 105,089,150 (100.0%)

Total basepairs processed: 10,614,004,150 bp
Quality-trimmed: 223,928,038 bp (2.1%)
Total written (filtered): 10,345,268,814 bp (97.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31907642 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
A: 29.0%
C: 30.8%
G: 18.8%
T: 21.4%
none/other: 0.0%

Overview of removed sequences
length count expect max.err error counts
1 22534133 26272287.5 0 22534133
2 7424483 6568071.9 0 7424483
3 1447916 1642018.0 0 1447916
4 343385 410504.5 0 343385
5 88652 102626.1 0 88652
6 13787 25656.5 0 13787
7 3613 6414.1 0 3613
8 2961 1603.5 0 2961
9 3515 400.9 0 2662 853
10 4242 100.2 1 2597 1645
11 3413 25.1 1 2440 973
12 2534 6.3 1 2396 138
13 2448 1.6 1 2395 53
14 2629 1.6 1 2583 46
15 2103 1.6 1 2054 49
16 1982 1.6 1 1930 52
17 1694 1.6 1 1620 74
18 1618 1.6 1 1568 50
19 895 1.6 1 861 34
20 1097 1.6 1 1054 43
21 873 1.6 1 848 25
22 864 1.6 1 826 38
23 1038 1.6 1 974 64
24 918 1.6 1 857 61
25 747 1.6 1 723 24
26 628 1.6 1 590 38
27 789 1.6 1 743 46
28 793 1.6 1 749 44
29 881 1.6 1 840 41
30 878 1.6 1 834 44
31 848 1.6 1 785 63
32 774 1.6 1 731 43
33 1003 1.6 1 965 38
34 769 1.6 1 733 36
35 993 1.6 1 934 59
36 688 1.6 1 646 42
37 891 1.6 1 843 48
38 470 1.6 1 432 38
39 572 1.6 1 541 31
40 416 1.6 1 370 46
41 505 1.6 1 477 28
42 222 1.6 1 176 46
43 196 1.6 1 173 23
44 138 1.6 1 94 44
45 216 1.6 1 185 31
46 193 1.6 1 157 36
47 130 1.6 1 88 42
48 153 1.6 1 101 52
49 126 1.6 1 95 31
50 87 1.6 1 69 18
51 81 1.6 1 49 32
52 118 1.6 1 73 45
53 79 1.6 1 51 28
54 47 1.6 1 17 30
55 60 1.6 1 19 41
56 71 1.6 1 46 25
57 55 1.6 1 29 26
58 63 1.6 1 33 30
59 42 1.6 1 28 14
60 50 1.6 1 12 38
61 49 1.6 1 26 23
62 74 1.6 1 39 35
63 74 1.6 1 52 22
64 58 1.6 1 41 17
65 74 1.6 1 40 34
66 65 1.6 1 34 31
67 83 1.6 1 41 42
68 49 1.6 1 33 16
69 92 1.6 1 62 30
70 105 1.6 1 52 53
71 63 1.6 1 39 24
72 50 1.6 1 16 34
73 37 1.6 1 5 32
74 37 1.6 1 4 33
75 27 1.6 1 3 24
76 32 1.6 1 2 30
77 20 1.6 1 0 20
78 52 1.6 1 0 52
79 29 1.6 1 1 28
80 38 1.6 1 0 38
81 59 1.6 1 2 57
82 59 1.6 1 0 59
83 40 1.6 1 0 40
84 35 1.6 1 0 35
85 33 1.6 1 0 33
86 56 1.6 1 0 56
87 66 1.6 1 0 66
88 39 1.6 1 0 39
89 51 1.6 1 0 51
90 54 1.6 1 0 54
91 30 1.6 1 0 30
92 40 1.6 1 0 40
93 14 1.6 1 0 14
94 133 1.6 1 1 132
95 45 1.6 1 0 45
96 31 1.6 1 0 31
97 56 1.6 1 0 56
98 30 1.6 1 0 30
99 9 1.6 1 0 9
100 21 1.6 1 0 21
101 68 1.6 1 0 68


RUN STATISTICS FOR INPUT FILE: SRR3192396_1.fastq.gz
=============================================
105089150 sequences processed in total

34 changes: 34 additions & 0 deletions src/multiqc/rna-seq/data/SRR3192396_1Log.final.out
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Started job on | May 03 04:15:10
Started mapping on | May 03 04:19:43
Finished on | May 03 05:44:43
Mapping speed, Million of reads per hour | 73.70

Number of input reads | 104413184
Average input read length | 196
UNIQUE READS:
Uniquely mapped reads number | 97833503
Uniquely mapped reads % | 93.70%
Average mapped length | 195.57
Number of splices: Total | 40714338
Number of splices: Annotated (sjdb) | 40114995
Number of splices: GT/AG | 40194421
Number of splices: GC/AG | 336796
Number of splices: AT/AC | 41871
Number of splices: Non-canonical | 141250
Mismatch rate per base, % | 0.25%
Deletion rate per base | 0.02%
Deletion average length | 1.56
Insertion rate per base | 0.01%
Insertion average length | 1.61
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 3659822
% of reads mapped to multiple loci | 3.51%
Number of reads mapped to too many loci | 11548
% of reads mapped to too many loci | 0.01%
UNMAPPED READS:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 2.77%
% of reads unmapped: other | 0.02%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
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