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Update trim galore to the latest Rust based version #1862

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d7c6547
Updating tools/trim_galore from version 0.6.10 to 0.6.11
Mar 2, 2026
1d2a9dc
another round of updates
bgruening May 11, 2026
5ee1f39
only output compressed fastq
bgruening May 12, 2026
244d99e
Update macros.xml
bgruening May 16, 2026
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14 changes: 9 additions & 5 deletions tools/trim_galore/macros.xml
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@@ -1,5 +1,5 @@
<macros>
<token name="@TOOL_VERSION@">0.6.10</token>
<token name="@TOOL_VERSION@">2.2.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
Expand All @@ -15,15 +15,19 @@
<conditional name="trimming">
<param name="trimming_select" type="select" label="Adapter sequence to be trimmed">
<option value="">Automatic detection</option>
<option value="--illumina">Illumina universal</option>
<option value="--nextera">Nextera transposase</option>
<option value="--illumina">Illumina universal (AGATCGGAAGAGC)</option>
<option value="--nextera">Nextera transposase (CTGTCTCTTATA)</option>
<option value="--small_rna">Illumina small RNA adapters</option>
<option value="--stranded_illumina">Stranded mRNA adapter (ACTGTCTCTTATA)</option>
<option value="--bgiseq">BGI/DNBSEQ adapter</option>
<option value="user">User defined adapter sequence</option>
</param>
<when value=""/>
<when value="--illumina"/>
<when value="--nextera"/>
<when value="--small_rna"/>
<when value="--stranded_illumina"/>
<when value="--bgiseq"/>
<when value="user">
<param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off">
<validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
Expand All @@ -38,7 +42,7 @@
<validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
</param>
</expand>
<param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
<param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help=""/>
<param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1">
<help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
Expand All @@ -60,7 +64,7 @@
publisher = {GitHub},
journal = {GitHub repository},
url = {https://https://github.com/FelixKrueger/TrimGalore.com/fenderglass/Flye}}
</citation>
</citation>
</citations>
</xml>
</macros>
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396 changes: 0 additions & 396 deletions tools/trim_galore/test-data/mec_reads_pair1.fastqsanger
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185 changes: 87 additions & 98 deletions tools/trim_galore/test-data/paired_collection_example_results3.txt
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@@ -1,52 +1,38 @@

SUMMARISING RUN PARAMETERS
==========================
=========================
Input filename: input_1.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 5.0
Python version: 3.12.10
Number of cores used for trimming: 4
Trim Galore version: 2.2.0 (Oxidized Edition)
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Adapter sequence: 'CTGTCTCTTATA' (user-specified or auto-detected)
Maximum trimming error rate: 0.1
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bp (default)


This is cutadapt 5.0 with Python 3.12.10
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
Processing single-end reads on 4 cores ...
Trim Galore 2.2.0 (Oxidized Edition) — adapter trimming built in
This is cutadapt 4.0 (compatible; for MultiQC backwards compatibility)
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
Processing reads on 1 core in single-end mode ...

=== Summary ===

Total reads processed: 99
Reads with adapters: 52 (52.5%)
Reads written (passing filters): 99 (100.0%)
Total reads processed: 99
Reads with adapters: 52 (52.5%)
Reads written (passing filters): 99 (100.0%)

Total basepairs processed: 24,849 bp
Quality-trimmed: 205 bp (0.8%)
Total written (filtered): 23,339 bp (93.9%)
Total basepairs processed: 24,849 bp
Quality-trimmed: 205 bp (0.8%)
Total written (filtered): 23,339 bp (93.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.

Minimum overlap: 1
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 9.6%
C: 38.5%
G: 23.1%
T: 28.8%
none/other: 0.0%

Overview of removed sequences
length count expect max.err error counts
1 11 24.8 0 11
Expand All @@ -57,80 +43,70 @@ length count expect max.err error counts
13 2 0.0 1 2
14 1 0.0 1 1
16 1 0.0 1 1
17 1 0.0 1 0 1
20 2 0.0 1 2
21 1 0.0 1 1
24 1 0.0 1 1
26 2 0.0 1 2
31 1 0.0 1 1
33 1 0.0 1 1
41 2 0.0 1 2
49 1 0.0 1 1
50 1 0.0 1 1
54 1 0.0 1 1
56 1 0.0 1 1
58 2 0.0 1 2
60 1 0.0 1 1
67 2 0.0 1 2
68 1 0.0 1 1
69 1 0.0 1 1
73 1 0.0 1 1
80 1 0.0 1 1
86 1 0.0 1 1
17 1 0.0 1 1
20 2 0.0 2 2
21 1 0.0 2 1
24 1 0.0 2 1
26 2 0.0 2 2
31 1 0.0 3 1
33 1 0.0 3 1
41 2 0.0 4 2
49 1 0.0 4 1
50 1 0.0 5 1
54 1 0.0 5 1
56 1 0.0 5 1
58 2 0.0 5 2
60 1 0.0 6 1
67 2 0.0 6 2
68 1 0.0 6 1
69 1 0.0 6 1
73 1 0.0 7 1
80 1 0.0 8 1
86 1 0.0 8 1


RUN STATISTICS FOR INPUT FILE: input_1.fastq
=============================================
99 sequences processed in total

Sequences removed because they became shorter than the length cutoff of 20 bp: 1 (1.0%)
Sequences removed because they were longer than the upper length cutoff: 0 (0.0%)
Sequences removed because of too many N bases: 0 (0.0%)

SUMMARISING RUN PARAMETERS
==========================
=========================
Input filename: input_2.fastq
Trimming mode: paired-end
Trim Galore version: 0.6.10
Cutadapt version: 5.0
Python version: 3.12.10
Number of cores used for trimming: 4
Trim Galore version: 2.2.0 (Oxidized Edition)
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Adapter sequence: 'CTGTCTCTTATA' (user-specified or auto-detected)
Maximum trimming error rate: 0.1
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Length cut-off for read 1: 35 bp (default)
Length cut-off for read 2: 35 bp (default)


This is cutadapt 5.0 with Python 3.12.10
Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
Processing single-end reads on 4 cores ...
Trim Galore 2.2.0 (Oxidized Edition) — adapter trimming built in
This is cutadapt 4.0 (compatible; for MultiQC backwards compatibility)
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
Processing reads on 1 core in single-end mode ...

=== Summary ===

Total reads processed: 99
Reads with adapters: 58 (58.6%)
Reads written (passing filters): 99 (100.0%)
Total reads processed: 99
Reads with adapters: 58 (58.6%)
Reads written (passing filters): 99 (100.0%)

Total basepairs processed: 24,849 bp
Quality-trimmed: 745 bp (3.0%)
Total written (filtered): 23,035 bp (92.7%)
Total basepairs processed: 24,849 bp
Quality-trimmed: 745 bp (3.0%)
Total written (filtered): 23,035 bp (92.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.

Minimum overlap: 1
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
A: 12.1%
C: 37.9%
G: 8.6%
T: 41.4%
none/other: 0.0%

Overview of removed sequences
length count expect max.err error counts
1 16 24.8 0 16
Expand All @@ -146,29 +122,42 @@ length count expect max.err error counts
16 1 0.0 1 1
17 1 0.0 1 1
19 2 0.0 1 2
21 1 0.0 1 1
25 1 0.0 1 1
30 1 0.0 1 1
32 2 0.0 1 2
34 1 0.0 1 1
36 2 0.0 1 2
38 1 0.0 1 1
40 1 0.0 1 1
41 1 0.0 1 1
42 1 0.0 1 1
43 1 0.0 1 1
49 1 0.0 1 1
51 1 0.0 1 1
56 1 0.0 1 1
57 1 0.0 1 1
60 1 0.0 1 1
67 1 0.0 1 1
80 1 0.0 1 1
21 1 0.0 2 1
25 1 0.0 2 1
30 1 0.0 3 1
32 2 0.0 3 2
34 1 0.0 3 1
36 2 0.0 3 2
38 1 0.0 3 1
40 1 0.0 4 1
41 1 0.0 4 1
42 1 0.0 4 1
43 1 0.0 4 1
49 1 0.0 4 1
51 1 0.0 5 1
56 1 0.0 5 1
57 1 0.0 5 1
60 1 0.0 6 1
67 1 0.0 6 1
80 1 0.0 8 1


RUN STATISTICS FOR INPUT FILE: input_2.fastq
=============================================
99 sequences processed in total
Sequences removed because they became shorter than the length cutoff of 20 bp: 1 (1.0%)
Sequences removed because they were longer than the upper length cutoff: 0 (0.0%)
Sequences removed because of too many N bases: 0 (0.0%)

=== Paired-end validation ===

Number of sequence pairs analysed: 99

Number of sequence pairs removed because at least one read was shorter than the length cutoff (1.01%):
1
Number of pairs removed for N content (0.00%):
0

Total number of sequences analysed for the sequence pair length validation: 99
Unpaired read 1 kept: 1
Unpaired read 2 kept: 0

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)
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