Adding back tool specific input output and index files

software/bowtie2/test/indices/E_coli/NC_010473.fa

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+../../../../../tests/data/fasta/E_coli/NC_010473.fa

software/bowtie2/test/input/Ecoli_DNA_R1.fastq.gz

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+../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

software/bowtie2/test/input/Ecoli_DNA_R2.fastq.gz

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+../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

software/bowtie2/test/input/test_R1_val_1.fq.gz

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+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

software/bowtie2/test/input/test_R2_val_2.fq.gz

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+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

software/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2_stats.txt

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+10000 reads; of these:
+  10000 (100.00%) were paired; of these:
+    893 (8.93%) aligned concordantly 0 times
+    8474 (84.74%) aligned concordantly exactly 1 time
+    633 (6.33%) aligned concordantly >1 times
+    ----
+    893 pairs aligned concordantly 0 times; of these:
+      815 (91.27%) aligned discordantly 1 time
+    ----
+    78 pairs aligned 0 times concordantly or discordantly; of these:
+      156 mates make up the pairs; of these:
+        0 (0.00%) aligned 0 times
+        1 (0.64%) aligned exactly 1 time
+        155 (99.36%) aligned >1 times
+100.00% overall alignment rate

software/bowtie2/test/output/test_GRCm38_bowtie2_stats.txt

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+9979 reads; of these:
+  9979 (100.00%) were paired; of these:
+    3584 (35.92%) aligned concordantly 0 times
+    3705 (37.13%) aligned concordantly exactly 1 time
+    2690 (26.96%) aligned concordantly >1 times
+    ----
+    3584 pairs aligned concordantly 0 times; of these:
+      886 (24.72%) aligned discordantly 1 time
+    ----
+    2698 pairs aligned 0 times concordantly or discordantly; of these:
+      5396 mates make up the pairs; of these:
+        2282 (42.29%) aligned 0 times
+        1467 (27.19%) aligned exactly 1 time
+        1647 (30.52%) aligned >1 times
+88.57% overall alignment rate

software/fastq_screen/test/input/test_R1.fastq.gz

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+../../../../tests/data/fastq/rna/test_R1.fastq.gz

software/fastq_screen/test/input/test_R1_val_1.fq.gz

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+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

software/fastq_screen/test/input/test_R2.fastq.gz

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+../../../../tests/data/fastq/rna/test_R2.fastq.gz

software/fastq_screen/test/input/test_R2_val_2.fq.gz

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+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

software/fastq_screen/test/input/test_single_end.fastq.gz

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+../../../../tests/data/fastq/rna/test_single_end.fastq.gz

software/fastq_screen/test/output/test_R1_screen.txt

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+#Fastq_screen version: 0.14.0	#Aligner: bowtie2	#Reads in subset: 100000
+Genome	#Reads_processed	#Unmapped	%Unmapped	#One_hit_one_genome	%One_hit_one_genome	#Multiple_hits_one_genome	%Multiple_hits_one_genome	#One_hit_multiple_genomes	%One_hit_multiple_genomes	Multiple_hits_multiple_genomes	%Multiple_hits_multiple_genomes
+Cat	10000	9171	91.71	0	0.00	0	0.00	421	4.21	408	4.08
+Chicken	10000	8932	89.32	0	0.00	0	0.00	64	0.64	1004	10.04
+Cow	10000	8484	84.84	0	0.00	0	0.00	294	2.94	1222	12.22
+Drosophila	10000	9469	94.69	0	0.00	0	0.00	19	0.19	512	5.12
+Human	10000	8367	83.67	2	0.02	3	0.03	354	3.54	1274	12.74
+Mouse	10000	122	1.22	3265	32.65	869	8.69	2066	20.66	3678	36.78
+Pig	10000	8459	84.59	0	0.00	0	0.00	334	3.34	1207	12.07
+Rat	10000	6432	64.32	1	0.01	3	0.03	1334	13.34	2230	22.30
+Zebrafish	10000	9125	91.25	0	0.00	0	0.00	41	0.41	834	8.34
+Arabidopsis	10000	9497	94.97	0	0.00	0	0.00	5	0.05	498	4.98
+Grape	10000	9600	96.00	0	0.00	1	0.01	82	0.82	317	3.17
+Potato	10000	9460	94.60	0	0.00	0	0.00	12	0.12	528	5.28
+Tomato	10000	9521	95.21	0	0.00	0	0.00	45	0.45	434	4.34
+Adapters	10000	10000	100.00	0	0.00	0	0.00	0	0.00	0	0.00
+Brachybacterium	10000	10000	100.00	0	0.00	0	0.00	0	0.00	0	0.00
+Pseudomonas	10000	10000	100.00	0	0.00	0	0.00	0	0.00	0	0.00
+Massilia_oculi	10000	9999	99.99	0	0.00	1	0.01	0	0.00	0	0.00
+Ecoli	10000	9998	99.98	1	0.01	1	0.01	0	0.00	0	0.00
+Lambda	10000	10000	100.00	0	0.00	0	0.00	0	0.00	0	0.00
+MT	10000	7856	78.56	0	0.00	0	0.00	2034	20.34	110	1.10
+PhiX	10000	10000	100.00	0	0.00	0	0.00	0	0.00	0	0.00
+rRNA	10000	9157	91.57	0	0.00	0	0.00	111	1.11	732	7.32
+Wasp	10000	9473	94.73	0	0.00	0	0.00	211	2.11	316	3.16
+Vectors	10000	9713	97.13	0	0.00	0	0.00	52	0.52	235	2.35
+Worm	10000	9645	96.45	0	0.00	0	0.00	13	0.13	342	3.42
+Yeast	10000	9507	95.07	0	0.00	0	0.00	4	0.04	489	4.89
+Mycoplasma	10000	9998	99.98	0	0.00	0	0.00	0	0.00	2	0.02
+
+%Hit_no_genomes: 0.88

software/fastqc/test/input/test_R1_val_1.fq.gz

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+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

software/fastqc/test/input/test_R2_val_2.fq.gz

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+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

software/hisat2/test/indices/E_coli/NC_010473.fa

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+../../../../../tests/data/fasta/E_coli/NC_010473.fa

software/hisat2/test/input/Ecoli_DNA_R1.fastq.gz

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+../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

software/hisat2/test/input/Ecoli_DNA_R2.fastq.gz

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+../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

software/hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

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+10000 reads; of these:
+  10000 (100.00%) were paired; of these:
+    823 (8.23%) aligned concordantly 0 times
+    8583 (85.83%) aligned concordantly exactly 1 time
+    594 (5.94%) aligned concordantly >1 times
+91.77% overall alignment rate

software/multiqc/test/input/bowtie2/test_GRCm38_bowtie2_stats.txt

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+../../../../bowtie2/test/output/test_GRCm38_bowtie2_stats.txt

software/multiqc/test/input/fastq_screen/test_R1_screen.txt

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+../../../../fastq_screen/test/output/test_R1_screen.txt

software/multiqc/test/input/fastqc/test_R1_fastqc.zip

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+../../../../fastqc/test/output/test_R1_fastqc.zip

software/multiqc/test/input/fastqc/test_R1_val_1_fastqc.zip

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+../../../../fastqc/test/output/test_R1_val_1_fastqc.zip

software/multiqc/test/input/fastqc/test_R2_fastqc.zip

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+../../../../fastqc/test/output/test_R2_fastqc.zip

software/multiqc/test/input/fastqc/test_R2_val_2_fastqc.zip

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+../../../../fastqc/test/output/test_R2_val_2_fastqc.zip

software/multiqc/test/input/hisat2/Ecoli_DNA_R_E_coli_hisat2_stats.txt

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+../../../../hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

software/multiqc/test/input/trim_galore/test_R1.fastq.gz_trimming_report.txt

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+../../../../trim_galore/test/output/test_R1.fastq.gz_trimming_report.txt

software/multiqc/test/input/trim_galore/test_R2.fastq.gz_trimming_report.txt

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+../../../../trim_galore/test/output/test_R2.fastq.gz_trimming_report.txt

software/trim_galore/test/input/test_R1.fastq.gz

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+../../../../tests/data/fastq/rna/test_R1.fastq.gz

software/trim_galore/test/input/test_R2.fastq.gz

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+../../../../tests/data/fastq/rna/test_R2.fastq.gz

software/trim_galore/test/output/test_R1.fastq.gz_trimming_report.txt

@@ -0,0 +1,97 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: test_R1.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.6.5
+Cutadapt version: 2.3
+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 smallRNA (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 2.3 with Python 3.7.3
+Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R1.fastq.gz
+Processing reads on 1 core in single-end mode ...
+Finished in 0.19 s (19 us/read; 3.12 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_R1.fastq.gz
+=============================================
+10000 sequences processed in total
+

software/trim_galore/test/output/test_R1_val_1.fq.gz

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+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

software/trim_galore/test/output/test_R2.fastq.gz_trimming_report.txt

@@ -0,0 +1,100 @@
+
+SUMMARISING RUN PARAMETERS
+==========================
+Input filename: test_R2.fastq.gz
+Trimming mode: paired-end
+Trim Galore version: 0.6.5
+Cutadapt version: 2.3
+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 smallRNA (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 2.3 with Python 3.7.3
+Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA test_R2.fastq.gz
+Processing reads on 1 core in single-end mode ...
+Finished in 0.22 s (22 us/read; 2.71 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_R2.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%)

software/trim_galore/test/output/test_R2_val_2.fq.gz

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+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz