diff --git a/software/fastqc/test/input/test_R1_val_1.fq.gz b/software/fastqc/test/input/test_R1_val_1.fq.gz deleted file mode 120000 index 88ccdc87..00000000 --- a/software/fastqc/test/input/test_R1_val_1.fq.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz \ No newline at end of file diff --git a/software/fastqc/test/input/test_R2_val_2.fq.gz b/software/fastqc/test/input/test_R2_val_2.fq.gz deleted file mode 120000 index 440be644..00000000 --- a/software/fastqc/test/input/test_R2_val_2.fq.gz +++ /dev/null @@ -1 +0,0 @@ -../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz \ No newline at end of file diff --git a/software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..2a6191a5 --- /dev/null +++ b/software/trimgalore/test/output/test_paired_end/test_1.fastq.gz_trimming_report.txt @@ -0,0 +1,97 @@ + +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 + diff --git a/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz b/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz new file mode 100644 index 00000000..5ed6d4d7 Binary files /dev/null and b/software/trimgalore/test/output/test_paired_end/test_1_val_1.fq.gz differ diff --git a/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..bd436f10 --- /dev/null +++ b/software/trimgalore/test/output/test_paired_end/test_2.fastq.gz_trimming_report.txt @@ -0,0 +1,100 @@ + +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%) diff --git a/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz b/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz new file mode 100644 index 00000000..a3ae7c03 Binary files /dev/null and b/software/trimgalore/test/output/test_paired_end/test_2_val_2.fq.gz differ diff --git a/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt b/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt new file mode 100644 index 00000000..85c2b6c5 --- /dev/null +++ b/software/trimgalore/test/output/test_single_end/test.fastq.gz_trimming_report.txt @@ -0,0 +1,61 @@ + +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%) + diff --git a/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz b/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz new file mode 100644 index 00000000..a1f8109c Binary files /dev/null and b/software/trimgalore/test/output/test_single_end/test_trimmed.fq.gz differ