mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
test(trimgalore): Refactor se and pe to use pytest-workflow
This commit is contained in:
Edmund Miller
parent
445498d0c3
commit
2fc39e02e2
13 changed files with 61 additions and 322 deletions
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_R1.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_R2.fastq.gz
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
../../../../tests/data/fastq/rna/test_single_end.fastq.gz
|
|
||||||
|
|
@ -1,36 +0,0 @@
|
||||||
#!/usr/bin/env nextflow
|
|
||||||
|
|
||||||
nextflow.enable.dsl = 2
|
|
||||||
|
|
||||||
include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
|
||||||
include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with single-end data
|
|
||||||
*/
|
|
||||||
workflow test_single_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:true ], // meta map
|
|
||||||
[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
TRIMGALORE_SE ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Test with paired-end data
|
|
||||||
*/
|
|
||||||
workflow test_paired_end {
|
|
||||||
|
|
||||||
def input = []
|
|
||||||
input = [ [ id:'test', single_end:false ], // meta map
|
|
||||||
[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
|
|
||||||
file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
|
|
||||||
|
|
||||||
TRIMGALORE_PE ( input )
|
|
||||||
}
|
|
||||||
|
|
||||||
workflow {
|
|
||||||
test_single_end()
|
|
||||||
test_paired_end()
|
|
||||||
}
|
|
||||||
|
|
@ -1,25 +0,0 @@
|
||||||
|
|
||||||
params {
|
|
||||||
outdir = "output/"
|
|
||||||
publish_dir_mode = "copy"
|
|
||||||
enable_conda = false
|
|
||||||
|
|
||||||
clip_r1 = 0
|
|
||||||
clip_r2 = 0
|
|
||||||
three_prime_clip_r1 = 0
|
|
||||||
three_prime_clip_r2 = 0
|
|
||||||
}
|
|
||||||
|
|
||||||
profiles {
|
|
||||||
conda {
|
|
||||||
params.enable_conda = true
|
|
||||||
}
|
|
||||||
docker {
|
|
||||||
docker.enabled = true
|
|
||||||
docker.runOptions = '-u \$(id -u):\$(id -g)'
|
|
||||||
}
|
|
||||||
singularity {
|
|
||||||
singularity.enabled = true
|
|
||||||
singularity.autoMounts = true
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,97 +0,0 @@
|
||||||
|
|
||||||
SUMMARISING RUN PARAMETERS
|
|
||||||
==========================
|
|
||||||
Input filename: test_1.fastq.gz
|
|
||||||
Trimming mode: paired-end
|
|
||||||
Trim Galore version: 0.6.4_dev
|
|
||||||
Cutadapt version: 2.6
|
|
||||||
Number of cores used for trimming: 1
|
|
||||||
Quality Phred score cutoff: 20
|
|
||||||
Quality encoding type selected: ASCII+33
|
|
||||||
Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
|
|
||||||
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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
|
|
||||||
Output file will be GZIP compressed
|
|
||||||
|
|
||||||
|
|
||||||
This is cutadapt 2.6 with Python 3.7.3
|
|
||||||
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_1.fastq.gz
|
|
||||||
Processing reads on 1 core in single-end mode ...
|
|
||||||
Finished in 0.64 s (64 us/read; 0.94 M reads/minute).
|
|
||||||
|
|
||||||
=== Summary ===
|
|
||||||
|
|
||||||
Total reads processed: 10,000
|
|
||||||
Reads with adapters: 3,225 (32.2%)
|
|
||||||
Reads written (passing filters): 10,000 (100.0%)
|
|
||||||
|
|
||||||
Total basepairs processed: 760,000 bp
|
|
||||||
Quality-trimmed: 4,492 bp (0.6%)
|
|
||||||
Total written (filtered): 748,403 bp (98.5%)
|
|
||||||
|
|
||||||
=== Adapter 1 ===
|
|
||||||
|
|
||||||
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
|
|
||||||
|
|
||||||
No. of allowed errors:
|
|
||||||
0-9 bp: 0; 10-12 bp: 1
|
|
||||||
|
|
||||||
Bases preceding removed adapters:
|
|
||||||
A: 23.8%
|
|
||||||
C: 28.2%
|
|
||||||
G: 22.7%
|
|
||||||
T: 25.3%
|
|
||||||
none/other: 0.0%
|
|
||||||
|
|
||||||
Overview of removed sequences
|
|
||||||
length count expect max.err error counts
|
|
||||||
1 2170 2500.0 0 2170
|
|
||||||
2 622 625.0 0 622
|
|
||||||
3 223 156.2 0 223
|
|
||||||
4 64 39.1 0 64
|
|
||||||
5 14 9.8 0 14
|
|
||||||
6 9 2.4 0 9
|
|
||||||
7 8 0.6 0 8
|
|
||||||
8 5 0.2 0 5
|
|
||||||
9 4 0.0 0 4
|
|
||||||
10 8 0.0 1 7 1
|
|
||||||
11 3 0.0 1 3
|
|
||||||
12 4 0.0 1 4
|
|
||||||
13 6 0.0 1 6
|
|
||||||
14 5 0.0 1 4 1
|
|
||||||
15 5 0.0 1 5
|
|
||||||
16 6 0.0 1 5 1
|
|
||||||
17 3 0.0 1 3
|
|
||||||
18 3 0.0 1 3
|
|
||||||
19 1 0.0 1 1
|
|
||||||
20 3 0.0 1 3
|
|
||||||
21 7 0.0 1 7
|
|
||||||
22 7 0.0 1 7
|
|
||||||
23 3 0.0 1 3
|
|
||||||
24 6 0.0 1 6
|
|
||||||
25 4 0.0 1 4
|
|
||||||
26 2 0.0 1 2
|
|
||||||
27 4 0.0 1 4
|
|
||||||
28 1 0.0 1 1
|
|
||||||
29 3 0.0 1 3
|
|
||||||
30 4 0.0 1 4
|
|
||||||
32 3 0.0 1 3
|
|
||||||
33 2 0.0 1 1 1
|
|
||||||
34 1 0.0 1 1
|
|
||||||
35 1 0.0 1 1
|
|
||||||
40 1 0.0 1 1
|
|
||||||
42 1 0.0 1 0 1
|
|
||||||
45 1 0.0 1 0 1
|
|
||||||
49 1 0.0 1 0 1
|
|
||||||
52 1 0.0 1 0 1
|
|
||||||
56 2 0.0 1 0 2
|
|
||||||
59 1 0.0 1 0 1
|
|
||||||
67 1 0.0 1 0 1
|
|
||||||
70 2 0.0 1 0 2
|
|
||||||
|
|
||||||
RUN STATISTICS FOR INPUT FILE: test_1.fastq.gz
|
|
||||||
=============================================
|
|
||||||
10000 sequences processed in total
|
|
||||||
|
|
||||||
Binary file not shown.
|
|
@ -1,100 +0,0 @@
|
||||||
|
|
||||||
SUMMARISING RUN PARAMETERS
|
|
||||||
==========================
|
|
||||||
Input filename: test_2.fastq.gz
|
|
||||||
Trimming mode: paired-end
|
|
||||||
Trim Galore version: 0.6.4_dev
|
|
||||||
Cutadapt version: 2.6
|
|
||||||
Number of cores used for trimming: 1
|
|
||||||
Quality Phred score cutoff: 20
|
|
||||||
Quality encoding type selected: ASCII+33
|
|
||||||
Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
|
|
||||||
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; 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
|
|
||||||
Output file will be GZIP compressed
|
|
||||||
|
|
||||||
|
|
||||||
This is cutadapt 2.6 with Python 3.7.3
|
|
||||||
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_2.fastq.gz
|
|
||||||
Processing reads on 1 core in single-end mode ...
|
|
||||||
Finished in 0.70 s (70 us/read; 0.86 M reads/minute).
|
|
||||||
|
|
||||||
=== Summary ===
|
|
||||||
|
|
||||||
Total reads processed: 10,000
|
|
||||||
Reads with adapters: 3,295 (33.0%)
|
|
||||||
Reads written (passing filters): 10,000 (100.0%)
|
|
||||||
|
|
||||||
Total basepairs processed: 760,000 bp
|
|
||||||
Quality-trimmed: 7,096 bp (0.9%)
|
|
||||||
Total written (filtered): 745,649 bp (98.1%)
|
|
||||||
|
|
||||||
=== Adapter 1 ===
|
|
||||||
|
|
||||||
Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
|
|
||||||
|
|
||||||
No. of allowed errors:
|
|
||||||
0-9 bp: 0; 10-12 bp: 1
|
|
||||||
|
|
||||||
Bases preceding removed adapters:
|
|
||||||
A: 22.6%
|
|
||||||
C: 28.2%
|
|
||||||
G: 23.6%
|
|
||||||
T: 25.6%
|
|
||||||
none/other: 0.0%
|
|
||||||
|
|
||||||
Overview of removed sequences
|
|
||||||
length count expect max.err error counts
|
|
||||||
1 2213 2500.0 0 2213
|
|
||||||
2 647 625.0 0 647
|
|
||||||
3 239 156.2 0 239
|
|
||||||
4 53 39.1 0 53
|
|
||||||
5 10 9.8 0 10
|
|
||||||
6 7 2.4 0 7
|
|
||||||
7 8 0.6 0 8
|
|
||||||
8 5 0.2 0 5
|
|
||||||
9 5 0.0 0 5
|
|
||||||
10 10 0.0 1 8 2
|
|
||||||
11 2 0.0 1 2
|
|
||||||
12 4 0.0 1 4
|
|
||||||
13 7 0.0 1 7
|
|
||||||
14 3 0.0 1 3
|
|
||||||
15 4 0.0 1 4
|
|
||||||
16 5 0.0 1 5
|
|
||||||
17 3 0.0 1 3
|
|
||||||
18 5 0.0 1 4 1
|
|
||||||
19 2 0.0 1 1 1
|
|
||||||
20 3 0.0 1 3
|
|
||||||
21 7 0.0 1 7
|
|
||||||
22 6 0.0 1 6
|
|
||||||
23 3 0.0 1 3
|
|
||||||
24 7 0.0 1 7
|
|
||||||
25 4 0.0 1 4
|
|
||||||
26 2 0.0 1 2
|
|
||||||
27 4 0.0 1 4
|
|
||||||
28 1 0.0 1 1
|
|
||||||
29 3 0.0 1 3
|
|
||||||
30 4 0.0 1 4
|
|
||||||
32 3 0.0 1 3
|
|
||||||
33 1 0.0 1 1
|
|
||||||
34 1 0.0 1 1
|
|
||||||
35 2 0.0 1 1 1
|
|
||||||
40 1 0.0 1 0 1
|
|
||||||
41 1 0.0 1 1
|
|
||||||
46 1 0.0 1 0 1
|
|
||||||
48 1 0.0 1 0 1
|
|
||||||
49 2 0.0 1 0 2
|
|
||||||
56 2 0.0 1 0 2
|
|
||||||
59 1 0.0 1 0 1
|
|
||||||
70 1 0.0 1 0 1
|
|
||||||
73 2 0.0 1 0 2
|
|
||||||
|
|
||||||
RUN STATISTICS FOR INPUT FILE: test_2.fastq.gz
|
|
||||||
=============================================
|
|
||||||
10000 sequences processed in total
|
|
||||||
|
|
||||||
Total number of sequences analysed for the sequence pair length validation: 10000
|
|
||||||
|
|
||||||
Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)
|
|
||||||
Binary file not shown.
|
|
@ -1,61 +0,0 @@
|
||||||
|
|
||||||
SUMMARISING RUN PARAMETERS
|
|
||||||
==========================
|
|
||||||
Input filename: test.fastq.gz
|
|
||||||
Trimming mode: single-end
|
|
||||||
Trim Galore version: 0.6.4_dev
|
|
||||||
Cutadapt version: 2.6
|
|
||||||
Number of cores used for trimming: 1
|
|
||||||
Quality Phred score cutoff: 20
|
|
||||||
Quality encoding type selected: ASCII+33
|
|
||||||
Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0, count Nextera: 0)
|
|
||||||
Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
|
|
||||||
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
|
|
||||||
Maximum trimming error rate: 0.1 (default)
|
|
||||||
Minimum required adapter overlap (stringency): 1 bp
|
|
||||||
Minimum required sequence length before a sequence gets removed: 20 bp
|
|
||||||
Output file will be GZIP compressed
|
|
||||||
|
|
||||||
|
|
||||||
This is cutadapt 2.6 with Python 3.7.3
|
|
||||||
Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz
|
|
||||||
Processing reads on 1 core in single-end mode ...
|
|
||||||
Finished in 0.06 s (28 us/read; 2.13 M reads/minute).
|
|
||||||
|
|
||||||
=== Summary ===
|
|
||||||
|
|
||||||
Total reads processed: 2,052
|
|
||||||
Reads with adapters: 223 (10.9%)
|
|
||||||
Reads written (passing filters): 2,052 (100.0%)
|
|
||||||
|
|
||||||
Total basepairs processed: 103,432 bp
|
|
||||||
Quality-trimmed: 11 bp (0.0%)
|
|
||||||
Total written (filtered): 103,117 bp (99.7%)
|
|
||||||
|
|
||||||
=== Adapter 1 ===
|
|
||||||
|
|
||||||
Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 223 times.
|
|
||||||
|
|
||||||
No. of allowed errors:
|
|
||||||
0-9 bp: 0; 10-13 bp: 1
|
|
||||||
|
|
||||||
Bases preceding removed adapters:
|
|
||||||
A: 31.8%
|
|
||||||
C: 37.7%
|
|
||||||
G: 16.1%
|
|
||||||
T: 14.3%
|
|
||||||
none/other: 0.0%
|
|
||||||
|
|
||||||
Overview of removed sequences
|
|
||||||
length count expect max.err error counts
|
|
||||||
1 190 513.0 0 190
|
|
||||||
2 3 128.2 0 3
|
|
||||||
3 16 32.1 0 16
|
|
||||||
4 10 8.0 0 10
|
|
||||||
5 4 2.0 0 4
|
|
||||||
|
|
||||||
RUN STATISTICS FOR INPUT FILE: test.fastq.gz
|
|
||||||
=============================================
|
|
||||||
2052 sequences processed in total
|
|
||||||
Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%)
|
|
||||||
|
|
||||||
Binary file not shown.
40
tests/software/trimgalore/main.nf
Normal file
40
tests/software/trimgalore/main.nf
Normal file
|
|
@ -0,0 +1,40 @@
|
||||||
|
#!/usr/bin/env nextflow
|
||||||
|
|
||||||
|
nextflow.enable.dsl = 2
|
||||||
|
|
||||||
|
include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
|
||||||
|
include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
|
||||||
|
|
||||||
|
/*
|
||||||
|
* Test with single-end data
|
||||||
|
*/
|
||||||
|
workflow test_trimgalore_single_end {
|
||||||
|
|
||||||
|
def input = []
|
||||||
|
input = [ [ id:'test', single_end:true ], // meta map
|
||||||
|
[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
||||||
|
|
||||||
|
TRIMGALORE_SE ( input )
|
||||||
|
}
|
||||||
|
|
||||||
|
// workflow test_trimgalore_single_end {
|
||||||
|
|
||||||
|
// def input = []
|
||||||
|
// input = [ [ id:'test', single_end:false ], // meta map
|
||||||
|
// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
|
||||||
|
|
||||||
|
// TRIMGALORE_SE ( input )
|
||||||
|
// }
|
||||||
|
|
||||||
|
/*
|
||||||
|
* Test with paired-end data
|
||||||
|
*/
|
||||||
|
workflow test_trimgalore_paired_end {
|
||||||
|
|
||||||
|
def input = []
|
||||||
|
input = [ [ id:'test', single_end:false ], // meta map
|
||||||
|
[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
|
||||||
|
file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
|
||||||
|
|
||||||
|
TRIMGALORE_PE ( input )
|
||||||
|
}
|
||||||
21
tests/software/trimgalore/test.yml
Normal file
21
tests/software/trimgalore/test.yml
Normal file
|
|
@ -0,0 +1,21 @@
|
||||||
|
- name: Run trimgalore single-end test workflow
|
||||||
|
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_single_end -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- trimgalore
|
||||||
|
files:
|
||||||
|
# These can't be md5'd reliably
|
||||||
|
# TODO Test for includes
|
||||||
|
- path: output/test_single_end/test.fastq.gz_trimming_report.txt
|
||||||
|
- path: output/test_single_end/test_trimmed.fq.gz
|
||||||
|
|
||||||
|
- name: Run trimgalore paired-end test workflow
|
||||||
|
command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_paired_end -c tests/config/nextflow.config
|
||||||
|
tags:
|
||||||
|
- trimgalore
|
||||||
|
files:
|
||||||
|
# These can't be md5'd reliably
|
||||||
|
# TODO Test for includes
|
||||||
|
- path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
|
||||||
|
- path: output/test_paired_end/test_1_val_1.fq.gz
|
||||||
|
- path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
|
||||||
|
- path: output/test_paired_end/test_2_val_2.fq.gz
|
||||||
Loading…
Reference in a new issue