mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +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
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../../../../tests/data/fastq/rna/test_R1.fastq.gz
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../../../../tests/data/fastq/rna/test_R2.fastq.gz
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../../../../tests/data/fastq/rna/test_single_end.fastq.gz
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@ -1,36 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { TRIMGALORE as TRIMGALORE_SE } from '../main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { TRIMGALORE as TRIMGALORE_PE } from '../main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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*/
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workflow test_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE_SE ( input )
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}
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/*
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* Test with paired-end data
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*/
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workflow test_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
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file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE_PE ( input )
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}
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workflow {
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test_single_end()
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test_paired_end()
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}
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@ -1,25 +0,0 @@
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params {
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outdir = "output/"
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publish_dir_mode = "copy"
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enable_conda = false
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clip_r1 = 0
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clip_r2 = 0
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three_prime_clip_r1 = 0
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three_prime_clip_r2 = 0
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}
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profiles {
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conda {
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params.enable_conda = true
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}
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docker {
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docker.enabled = true
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docker.runOptions = '-u \$(id -u):\$(id -g)'
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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}
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}
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@ -1,97 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_1.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.4_dev
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Cutadapt version: 2.6
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.6 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_1.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.64 s (64 us/read; 0.94 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,225 (32.2%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 4,492 bp (0.6%)
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Total written (filtered): 748,403 bp (98.5%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3225 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 23.8%
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C: 28.2%
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G: 22.7%
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T: 25.3%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2170 2500.0 0 2170
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2 622 625.0 0 622
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3 223 156.2 0 223
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4 64 39.1 0 64
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5 14 9.8 0 14
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6 9 2.4 0 9
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 4 0.0 0 4
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10 8 0.0 1 7 1
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11 3 0.0 1 3
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12 4 0.0 1 4
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13 6 0.0 1 6
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14 5 0.0 1 4 1
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15 5 0.0 1 5
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16 6 0.0 1 5 1
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17 3 0.0 1 3
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18 3 0.0 1 3
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19 1 0.0 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 7 0.0 1 7
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23 3 0.0 1 3
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24 6 0.0 1 6
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 2 0.0 1 1 1
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34 1 0.0 1 1
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35 1 0.0 1 1
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40 1 0.0 1 1
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42 1 0.0 1 0 1
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45 1 0.0 1 0 1
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49 1 0.0 1 0 1
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52 1 0.0 1 0 1
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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67 1 0.0 1 0 1
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70 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_1.fastq.gz
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=============================================
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10000 sequences processed in total
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Binary file not shown.
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test_2.fastq.gz
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Trimming mode: paired-end
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Trim Galore version: 0.6.4_dev
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Cutadapt version: 2.6
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Using Nextera adapter for trimming (count: 83). Second best hit was Illumina (count: 0)
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Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.6 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_2.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.70 s (70 us/read; 0.86 M reads/minute).
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=== Summary ===
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Total reads processed: 10,000
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Reads with adapters: 3,295 (33.0%)
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Reads written (passing filters): 10,000 (100.0%)
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Total basepairs processed: 760,000 bp
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Quality-trimmed: 7,096 bp (0.9%)
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Total written (filtered): 745,649 bp (98.1%)
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=== Adapter 1 ===
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Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 3295 times.
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No. of allowed errors:
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0-9 bp: 0; 10-12 bp: 1
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Bases preceding removed adapters:
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A: 22.6%
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C: 28.2%
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G: 23.6%
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T: 25.6%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 2213 2500.0 0 2213
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2 647 625.0 0 647
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3 239 156.2 0 239
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4 53 39.1 0 53
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5 10 9.8 0 10
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6 7 2.4 0 7
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7 8 0.6 0 8
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8 5 0.2 0 5
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9 5 0.0 0 5
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10 10 0.0 1 8 2
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11 2 0.0 1 2
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12 4 0.0 1 4
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13 7 0.0 1 7
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14 3 0.0 1 3
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15 4 0.0 1 4
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16 5 0.0 1 5
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17 3 0.0 1 3
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18 5 0.0 1 4 1
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19 2 0.0 1 1 1
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20 3 0.0 1 3
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21 7 0.0 1 7
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22 6 0.0 1 6
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23 3 0.0 1 3
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24 7 0.0 1 7
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25 4 0.0 1 4
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26 2 0.0 1 2
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27 4 0.0 1 4
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28 1 0.0 1 1
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29 3 0.0 1 3
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30 4 0.0 1 4
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32 3 0.0 1 3
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33 1 0.0 1 1
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34 1 0.0 1 1
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35 2 0.0 1 1 1
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40 1 0.0 1 0 1
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41 1 0.0 1 1
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46 1 0.0 1 0 1
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48 1 0.0 1 0 1
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49 2 0.0 1 0 2
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56 2 0.0 1 0 2
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59 1 0.0 1 0 1
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70 1 0.0 1 0 1
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73 2 0.0 1 0 2
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RUN STATISTICS FOR INPUT FILE: test_2.fastq.gz
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=============================================
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10000 sequences processed in total
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Total number of sequences analysed for the sequence pair length validation: 10000
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Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21 (0.21%)
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Binary file not shown.
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@ -1,61 +0,0 @@
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SUMMARISING RUN PARAMETERS
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==========================
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Input filename: test.fastq.gz
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Trimming mode: single-end
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Trim Galore version: 0.6.4_dev
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Cutadapt version: 2.6
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Number of cores used for trimming: 1
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Quality Phred score cutoff: 20
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Quality encoding type selected: ASCII+33
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Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0, count Nextera: 0)
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Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).
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Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))
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Maximum trimming error rate: 0.1 (default)
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Minimum required adapter overlap (stringency): 1 bp
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Minimum required sequence length before a sequence gets removed: 20 bp
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Output file will be GZIP compressed
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This is cutadapt 2.6 with Python 3.7.3
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Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC test.fastq.gz
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Processing reads on 1 core in single-end mode ...
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Finished in 0.06 s (28 us/read; 2.13 M reads/minute).
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=== Summary ===
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Total reads processed: 2,052
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Reads with adapters: 223 (10.9%)
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Reads written (passing filters): 2,052 (100.0%)
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Total basepairs processed: 103,432 bp
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Quality-trimmed: 11 bp (0.0%)
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Total written (filtered): 103,117 bp (99.7%)
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=== Adapter 1 ===
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Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 223 times.
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No. of allowed errors:
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0-9 bp: 0; 10-13 bp: 1
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Bases preceding removed adapters:
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A: 31.8%
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C: 37.7%
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G: 16.1%
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T: 14.3%
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none/other: 0.0%
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Overview of removed sequences
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length count expect max.err error counts
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1 190 513.0 0 190
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2 3 128.2 0 3
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3 16 32.1 0 16
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4 10 8.0 0 10
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5 4 2.0 0 4
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RUN STATISTICS FOR INPUT FILE: test.fastq.gz
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=============================================
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2052 sequences processed in total
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Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%)
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Binary file not shown.
40
tests/software/trimgalore/main.nf
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40
tests/software/trimgalore/main.nf
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@ -0,0 +1,40 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { TRIMGALORE as TRIMGALORE_SE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
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include { TRIMGALORE as TRIMGALORE_PE } from '../../../software/trimgalore/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )
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/*
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* Test with single-end data
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*/
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workflow test_trimgalore_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE_SE ( input )
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}
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// workflow test_trimgalore_single_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// [ file("${launchDir}/tests/data/fastq/rna/test_single_end.fastq.gz", checkIfExists: true) ] ]
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// TRIMGALORE_SE ( input )
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// }
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/*
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* Test with paired-end data
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*/
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workflow test_trimgalore_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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[ file("${launchDir}/tests/data/fastq/rna/test_R1.fastq.gz", checkIfExists: true),
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file("${launchDir}/tests/data/fastq/rna/test_R2.fastq.gz", checkIfExists: true) ] ]
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TRIMGALORE_PE ( input )
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}
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21
tests/software/trimgalore/test.yml
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21
tests/software/trimgalore/test.yml
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- name: Run trimgalore single-end test workflow
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command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_single_end -c tests/config/nextflow.config
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tags:
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- trimgalore
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files:
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# These can't be md5'd reliably
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# TODO Test for includes
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- path: output/test_single_end/test.fastq.gz_trimming_report.txt
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- path: output/test_single_end/test_trimmed.fq.gz
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- name: Run trimgalore paired-end test workflow
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command: nextflow run ./tests/software/trimgalore/ -profile docker -entry test_trimgalore_paired_end -c tests/config/nextflow.config
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tags:
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- trimgalore
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files:
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# These can't be md5'd reliably
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# TODO Test for includes
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- path: output/test_paired_end/test_1.fastq.gz_trimming_report.txt
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- path: output/test_paired_end/test_1_val_1.fq.gz
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- path: output/test_paired_end/test_2.fastq.gz_trimming_report.txt
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- path: output/test_paired_end/test_2_val_2.fq.gz
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