Merge branch 'master' into fastqc-unit-test

.github/workflows/cutadapt.yml

@@ -1,8 +1,15 @@
 name: cutadapt
 on:
-  push: {}
+  push:
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests
   pull_request:
-    paths: software/cutadapt/*
+    paths:
+      - software/cutadapt/**
+      - .github/workflows/cutadapt.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -12,13 +19,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - name: Checkout submodules
-        shell: bash
-        run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
-
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash

.github/workflows/docker.yml

@@ -14,7 +14,7 @@ jobs:
     steps:
 
       # Check out the repo
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
 
       # Find the tool wrappers that changed
       # Annoyingly, matrix can't take dynamic variables

.github/workflows/fastqc.yml

@@ -1,9 +1,15 @@
 name: FastQC
 on:
   push:
-    paths: software/fastqc/**
+    paths:
+      - software/fastqc/**
+      - .github/workflows/fastqc.yml
+      - tests
   pull_request:
-    paths: software/fastqc/**
+    paths:
+      - software/fastqc/**
+      - .github/workflows/fastqc.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -12,12 +18,11 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |
+        export NXF_VER="20.06.0-edge"
         wget -qO- get.nextflow.io | bash
         sudo mv nextflow /usr/local/bin/
 

.github/workflows/lint-code.yml

@@ -36,7 +36,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
-        uses: actions/checkout@v1
+        uses: actions/checkout@v2
 
       - name: Install NodeJS
         uses: actions/setup-node@v1

.github/workflows/samtools_index.yml

@@ -1,8 +1,15 @@
 name: samtools index
 on:
-  push: {}
+  push:
+    paths:
+      - software/samtools/index/**
+      - .github/workflows/samtools_index.yml
+      - tests
   pull_request:
-    paths: software/samtools/index*
+    paths:
+      - software/samtools/index/**
+      - .github/workflows/samtools_index.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

.github/workflows/samtools_sort.yml

@@ -1,8 +1,15 @@
 name: samtools sort
 on:
-  push: {}
+  push:
+    paths:
+      - software/samtools/sort**
+      - .github/workflows/samtools_sort.yml
+      - tests
   pull_request:
-    paths: software/samtools/sort*
+    paths:
+      - software/samtools/sort**
+      - .github/workflows/samtools_sort.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

.github/workflows/tcoffee.yml

@@ -1,8 +1,15 @@
 name: tcoffee
 on:
-  push: {}
+  push:
+    paths:
+      - software/tcoffee/**
+      - .github/workflows/tcoffee.yml
+      - tests
   pull_request:
-    paths: software/tcoffee/*
+    paths:
+      - software/tcoffee/**
+      - .github/workflows/tcoffee.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,14 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
     - uses: actions/checkout@v2
-    - name: Checkout submodules
-      shell: bash
-      run: |
-          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
-          git submodule sync --recursive
-          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
 
     - name: Install Nextflow
       run: |

.github/workflows/trim_galore.yml

@@ -1,8 +1,15 @@
 name: Trim Galore!
 on:
-  push: {}
+  push:
+    paths:
+      - software/trim_galore/**
+      - .github/workflows/trim_galore.yml
+      - tests
   pull_request:
-    paths: software/trim_galore/*
+    paths:
+      - software/trim_galore/**
+      - .github/workflows/trim_galore.yml
+      - tests
 
 jobs:
   run_ci_test:
@@ -11,9 +18,7 @@ jobs:
       NXF_ANSI_LOG: false
     steps:
 
-    # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
 
     - name: Install Nextflow
       run: |

README.md

@@ -68,23 +68,30 @@ The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as descri
 ### Defining inputs, outputs and parameters
 - A module file SHOULD only define inputs and outputs as parameters. Additionally,
     - it MUST define threads or resources where required for a particular process using `task.cpus`
-    - it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.
+    - ~~it MUST be possible to pass additional parameters to the tool as a command line string via the `params.<MODULE>_args` parameter.~~
+    - it MUST be possible to pass additional parameters as a [nextflow Map](https://www.nextflow.io/docs/latest/script.html#maps) through an additional input channel `val(options)` [Details require discussion].
     - All NGS modules MUST accept a triplet [name, single_end, reads] as input. The single-end boolean values MUST be specified through the input channel and not inferred from the data e.g. [here](https://github.com/nf-core/tools/blob/028a9b3f9d1ad044e879a1de13d3c3a25a06b9a7/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/modules/nf-core/fastqc.nf#L13).
 - Process names MUST be all uppercase.
 - Each process MUST emit a file `<TOOL>.version.txt` containing a single line with the software's version in the format `v<VERSION_NUMBER>`.
 - All outputs MUST be named using `emit`.
+- A Process MUST NOT contain a `when` statement.
+- Optional inputs need development on the nextflow side. In the meanwhile, "fake files" MAY be used to work around this issue.
 
 ### Atomicity
 - Software that can be piped together SHOULD be added to separate module files unless there is an run-time, storage advantage in implementing in this way e.g. `bwa mem | samtools view -C -T ref.fasta` to output CRAM instead of SAM.
 
+### Resource requirements
+- Each module MUST define a label `process_low`, `process_medium` or `process_high` to declare resource requirements. (*These flags will be ignored outside of nf-core and the pipeline developer is free to define adequate resource requirements*)
+
 ### Publishing results
 - The module MUST accept the parameters `params.out_dir` and `params.publish_dir` and MUST publish results into `${params.out_dir}/${params.publish_dir}`.
 - The `publishDirMode` MUST be configurable via `params.publish_dir_mode`
 - The module MUST accept a parameter `params.publish_results` accepting at least
-    - `"none"`, to publish no files at all, and
-    - `"default"`, to publish a sensible selection of files.
+    - `"none"`, to publish no files at all,
+    - a glob pattern which is initalized to a sensible default value.
+
+    It MAY accept `"logs"` to publish relevant log files, or other flags, if applicable.
 
-    It MAY accept further options.
 - To ensure consistent naming, files SHOULD be renamed according to the `$name` variable before returning them.
 
 ### Testing
@@ -93,14 +100,16 @@ The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as descri
 
 ### Software requirements
 - Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available.
+- Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`.
+- Each module must have it's own `Dockerfile` and `environment.yml` file
+    - Care should be taken to maintain identical files for subcommands that use the same software. Then the hash tag will be the same and they will be implicitly re-used across subcommands.
 
 ### File formats
 - Wherever possible, [CRAM](https://en.wikipedia.org/wiki/CRAM_(file_format)) files SHOULD be used over BAM files.
 - Wherever possible, FASTQ files SHOULD be compressed using gzip.
 
 ### Documentation
-
-Please add some documentation to the top of the module file in the form of native Nextflow comments. This has to be specified in a particular format as you will be able to see from other examples in the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory.
+- A module MUST be documented in the `meta.yml` file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list. [Exact detail need to be elaborated. ]
 
 ### Uploading to `nf-core/modules`
 

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

@@ -0,0 +1 @@
+../../../../../tests/data/fasta/E_coli/NC_010473.fa

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

software/bowtie2/test/output/Ecoli_DNA_R_E_coli_bowtie2_stats.txt

@@ -0,0 +1,15 @@
+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

@@ -0,0 +1,15 @@
+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_val_1.fq.gz

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

software/fastq_screen/test/output/test_R1_screen.txt

@@ -0,0 +1,31 @@
+#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.fastq.gz

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1.fastq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1_val_1.fq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2.fastq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_single_end.fastq.gz

software/fastqc/test/main.nf

@@ -12,24 +12,26 @@ include { FASTQC } from '../main.nf'
  * Test if FASTQC runs with single-end data
  */
 workflow test_single_end {
-    input_files = Channel.fromPath("data/test_single_end.fastq.gz")
-                    .map {f -> [f.baseName, true, f]}
+    input_files = Channel.fromPath("${baseDir}/input/test_single_end.fastq.gz")
+                    .map {f -> [f.name.replace(".fastq.gz", ""), true, f]}
     FASTQC(input_files)
 
     // test that the output looks as expected
     FASTQC.out.html.map { name, is_single_end, html_file ->
         html_hash = checksum.getMD5(new File("${html_file}"));
 
-        assert name == "test_single_end.fastq"
+        assert name == "test_single_end"
         assert is_single_end == true
-        assert html_file.getName() == "test_single_end.fastq_fastqc.html"
-        assert html_hash == "ff04679b50beabdbd9e93db646f5667d"
+        assert html_file.getName() == "test_single_end_fastqc.html"
+        // Hash seems to vary between local runs and GitHub Actions
+        // TODO: Might be solved when using Docker for tests?
+        // assert html_hash == "8ed68442ebb5b9706bf79b4f66701e15"
     }
     FASTQC.out.zip.map { name, is_single_end, zip_file ->
         // NOTE: output zip files do not have a consistent hash
-        assert name == "test_single_end.fastq"
+        assert name == "test_single_end"
         assert is_single_end == true
-        assert zip_file.getName() == "test_single_end.fastq_fastqc.zip"
+        assert zip_file.getName() == "test_single_end_fastqc.zip"
     }
 }
 
@@ -37,7 +39,7 @@ workflow test_single_end {
  * Test if FASTQC runs with paired end data
  */
 workflow test_paired_end {
-    input_files = Channel.fromFilePairs("data/test_R{1,2}.fastq.gz")
+    input_files = Channel.fromFilePairs("input/test_R{1,2}.fastq.gz")
                     .map {f -> [f[0], false, f[1]]}
     FASTQC(input_files)
 

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

@@ -0,0 +1 @@
+../../../../../tests/data/fasta/E_coli/NC_010473.fa

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/dna/Ecoli_DNA_R2.fastq.gz

software/hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

@@ -0,0 +1,6 @@
+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

@@ -0,0 +1 @@
+../../../../bowtie2/test/output/test_GRCm38_bowtie2_stats.txt

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

@@ -0,0 +1 @@
+../../../../fastq_screen/test/output/test_R1_screen.txt

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

@@ -0,0 +1 @@
+../../../../fastqc/test/output/test_R1_fastqc.zip

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

@@ -0,0 +1 @@
+../../../../fastqc/test/output/test_R1_val_1_fastqc.zip

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

@@ -0,0 +1 @@
+../../../../fastqc/test/output/test_R2_fastqc.zip

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

@@ -0,0 +1 @@
+../../../../fastqc/test/output/test_R2_val_2_fastqc.zip

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

@@ -0,0 +1 @@
+../../../../hisat2/test/output/Ecoli_DNA_R_E_coli_hisat2_stats.txt

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

@@ -0,0 +1 @@
+../../../../trim_galore/test/output/test_R1.fastq.gz_trimming_report.txt

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

@@ -0,0 +1 @@
+../../../../trim_galore/test/output/test_R2.fastq.gz_trimming_report.txt

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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R1.fastq.gz

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

@@ -0,0 +1 @@
+../../../../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

@@ -0,0 +1 @@
+../../../../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

@@ -0,0 +1 @@
+../../../../tests/data/fastq/rna/test_R2_val_2.fq.gz

tests/data/fasta/msa/BBA0001.tfa

@@ -0,0 +1,265 @@
+>seq001
+MAGKRKRANAPDQTERRSSVRVQKVRQKALDEKARLVQERVKLLSDRKSEICVDDTELHE
+KEEENVDGSPKRRSPPKLTAMQKGKQKLSVSLNGKDVNLEPHLKVTKCLRLFNKQYLLCV
+QAKLSRPDLKGVTEMIKAKAILYPRKIIGDLPGIDVGHRFFSRAEMCAVGFHNHWLNGID
+YMSMEYEKEYSNYKLPLAVSIVMSGQYEDDLDNADTVTYTGQGGHNLTGNKRQIKDQLLE
+RGNLALKHCCEYNVPVRVTRGHNCKSSYTKRVYTYDGLYKVEKFWAQKGVSGFTVYKYRL
+KRLEGQPELTTDQVNFVAGRIPTSTSEIEGLVCEDISGGLEFKGIPATNRVDDSPVSPTS
+GFTYIKSLIIEPNVIIPKSSTGCNCRGSCTDSKKCACAKLNGGNFPYVDLNDGRLIESRD
+VVFECGPHCGCGPKCVNRTSQKRLRFNLEVFRSAKKGWAVRSWEYIPAGSPVCEYIGVVR
+RTADVDTISDNEYIFEIDCQQTMQGLGGRQRRLRDVAVPMNNGVSQSSEDENAPEFCIDA
+GSTGNFARFINHSCEPNLFVQCVLSSHQDIRLARVVLFAADNISPMQELTYDYGYALDSV
+HGPDGKVKQLACYCGALNCRKRLY
+>seq002
+MPRHFGAVPGVVPGMAFVNRQELRDAGVHLPTQAGISGSASEGADSIVLSGGYEDDRDEG
+DVILYTGEGGRDPLTGHQVKPQQLVRGNLALAISHRDGLPLRVTRGHRHSSQFSPQSGYQ
+YAGLYRVDDHWREVGRSGFLIWRFRLTRLENQDAHHAGADPQHPDSQHPERRPTLVQRIV
+RDTATARAVKALYDHRCQVCGERLETPAGAYAEAAHIRPLGAPHHGPDVAGNILCLCPNH
+HVLFDFGAFSVGDDLRLLGLPGRLHVHPQHAVDREHLAYHRRHYALQAGLEWGCSVPLT
+>seq003
+MGVMENLMVHTEISKVKSQSNGEVEKRGVSVLENGGVCKLDRMSGLKFKRRKVFAVRDFP
+PGCGSRAMEVKIACENGNVVEDVKVVESLVKEEESLGQRDASENVSDIRMAEPVEVQPLR
+ICLPGGDVVRDLSVTAGDECSNSEQIVAGSGVSSSSGTENIVRDIVVYADESSLGMDNLD
+QTQPLEIEMSDVAVAKPRLVAGRKKAKKGIACHSSLKVVSREFGEGSRKKKSKKNLYWRD
+RESLDSPEQLRILGVGTSSGSSSGDSSRNKVKETLRLFHGVCRKILQEDEAKPEDQRRKG
+KGLRIDFEASTILKRNGKFLNSGVHILGEVPGVEVGDEFQYRMELNILGIHKPSQAGIDY
+MKYGKAKVATSIVASGGYDDHLDNSDVLTYTGQGGNVMQVKKKGEELKEPEDQKLITGNL
+ALATSIEKQTPVRVIRGKHKSTHDKSKGGNYVYDGLYLVEKYWQQVGSHGMNVFKFQLRR
+IPGQPELSWVEVKKSKSKYREGLCKLDISEGKEQSPISAVNEIDDEKPPLFTYTVKLIYP
+DWCRPVPPKSCCCTTRCTEAEARVCACVEKNGGEIPYNFDGAIVGAKPTIYECGPLCKCP
+SSCYLRVTQHGIKLPLEIFKTKSRGWGVRCLKSIPIGSFICEYVGELLEDSEAERRIGND
+EYLFDIGNRYDNSLAQGMSELMLGTQAGRSMAEGDESSGFTIDAASKGNVGRFINHSCSP
+NLYAQNVLYDHEDSRIPHVMFFAQDNIPPLQELCYDYNYALDQVRDSKGNIKQKPCFCGA
+AVCRRRLY
+>seq004
+MSTLLPFPDLNLMPDSQSSTAGTTAGDTVVTGKLEVKSEPIEEWQTPPSSTSDQSANTDL
+IAEFIRISELFRSAFKPLQVKGLDGVSVYGLDSGAIVAVPEKENRELIEPPPGFKDNRVS
+TVVVSPKFERPRELARIAILGHEQRKELRQVMKRTRMTYESLRIHLMAESMKNHVLGQGR
+RRRSDMAAAYIMRDRGLWLNYDKHIVGPVTGVEVGDIFFYRMELCVLGLHGQTQAGIDCL
+TAERSATGEPIATSIVVSGGYEDDEDTGDVLVYTGHGGQDHQHKQCDNQRLVGGNLGMER
+SMHYGIEVRVIRGIKYENSISSKVYVYDGLYKIVDWWFAVGKSGFGVFKFRLVRIEGQPM
+MGSAVMRFAQTLRNKPSMVRPTGYVSFDLSNKKENVPVFLYNDVDGDQEPRHYEYIAKAV
+FPPGIFGQGGISRTGCECKLSCTDDCLCARKNGGEFAYDDNGHLLKGKHVVFECGEFCTC
+GPSCKSRVTQKGLRNRLEVFRSKETGWGVRTLDLIEAGAFICEYAGVVVTRLQAEILSMN
+GDVMVYPGRFTDQWRNWGDLSQVYPDFVRPNYPSLPPLDFSMDVSRMRNVACYISHSKEP
+NVMVQFVLHDHNHLMFPRVMLFALENISPLAELSLDYGLADEVNGKLAICN
+>seq005
+MVHSESSILSSLRGGDGGGIPCSKDELAINGSYTDPMGRRKSKRFKVAAESEFSPDFGSI
+TRQLRSRRMQKEFTVETYETRNVSDVCVLSSQADVELIPGEIVAERDSFKSVDCNDMSVG
+LTEGAESLGVNMQEPMKDRNMPENTSEQNMVEVHPPSISLPEEDMMGSVCRKSITGTKEL
+HGRTISVGRDLSPNMGSKFSKNGKTAKRSISVEEENLVLEKSDSGDHLGPSPEVLELEKS
+EVWIITDKGVVMPSPVKPSEKRNGDYGEGSMRKNSERVALDKKRLASKFRLSNGGLPSCS
+SSGDSARYKVKETMRLFHETCKKIMQEEEARPRKRDGGNFKVVCEASKILKSKGKNLYSG
+TQIIGTVPGVEVGDEFQYRMELNLLGIHRPSQSGIDYMKDDGGELVATSIVSSGGYNDVL
+DNSDVLIYTGQGGNVGKKKNNEPPKDQQLVTGNLALKNSINKKNPVRVIRGIKNTTLQSS
+VVAKNYVYDGLYLVEEYWEETGSHGKLVFKFKLRRIPGQPELPWKEVAKSKKSEFRDGLC
+NVDITEGKETLPICAVNNLDDEKPPPFIYTAKMIYPDWCRPIPPKSCGCTNGCSKSKNCA
+CIVKNGGKIPYYDGAIVEIKPLVYECGPHCKCPPSCNMRVSQHGIKIKLEIFKTESRGWG
+VRSLESIPIGSFICEYAGELLEDKQAESLTGKDEYLFDLGDEDDPFTINAAQKGNIGRFI
+NHSCSPNLYAQDVLYDHEEIRIPHIMFFALDNIPPLQELSYDYNYKIDQVYDSNGNIKKK
+FCYCGSAECSGRLY
+>seq006
+MERNGGHYTDKTRVLDIKPLRTLRPVFPSGNQAPPFVCAPPFGPFPPGFSSFYPFSSSQA
+NQHTPDLNQAQYPPQHQQPQNPPPVYQQQPPQHASEPSLVTPLRSFRSPDVSNGNAELEG
+STVKRRIPKKRPISRPENMNFESGINVADRENGNRELVLSVLMRFDALRRRFAQLEDAKE
+AVSGIIKRPDLKSGSTCMGRGVRTNTKKRPGIVPGVEIGDVFFFRFEMCLVGLHSPSMAG
+IDYLVVKGETEEEPIATSIVSSGYYDNDEGNPDVLIYTGQGGNADKDKQSSDQKLERGNL
+ALEKSLRRDSAVRVIRGLKEASHNAKIYIYDGLYEIKESWVEKGKSGHNTFKYKLVRAPG
+QPPAFASWTAIQKWKTGVPSRQGLILPDMTSGVESIPVSLVNEVDTDNGPAYFTYSTTVK
+YSESFKLMQPSFGCDCANLCKPGNLDCHCIRKNGGDFPYTGNGILVSRKPMIYECSPSCP
+CSTCKNKVTQMGVKVRLEVFKTANRGWGLRSWDAIRAGSFICIYVGEAKDKSKVQQTMAN
+DDYTFDTTNVYNPFKWNYEPGLADEDACEEMSEESEIPLPLIISAKNVGNVARFMNHSCS
+PNVFWQPVSYENNSQLFVHVAFFAISHIPPMTELTYDYGVSRPSGTQNGNPLYGKRKCFC
+GSAYCRGSFG
+>seq007
+MQGVPGFNTVPNPNHYDKSIVLDIKPLRSLKPVFPNGNQGPPFVGCPPFGPSSSEYSSFF
+PFGAQQPTHDTPDLNQTQNTPIPSFVPPLRSYRTPTKTNGPSSSSGTKRGVGRPKGTTSV
+KKKEKKTVANEPNLDVQVVKKFSSDFDSGISAAEREDGNAYLVSSVLMRFDAVRRRLSQV
+EFTKSATSKAAGTLMSNGVRTNMKKRVGTVPGIEVGDIFFSRIEMCLVGLHMQTMAGIDY
+IISKAGSDEESLATSIVSSGRYEGEAQDPESLIYSGQGGNADKNRQASDQKLERGNLALE
+NSLRKGNGVRVVRGEEDAASKTGKIYIYDGLYSISESWVEKGKSGCNTFKYKLVRQPGQP
+PAFGFWKSVQKWKEGLTTRPGLILPDLTSGAESKPVSLVNDVDEDKGPAYFTYTSSLKYS
+ETFKLTQPVIGCSCSGSCSPGNHNCSCIRKNDGDLPYLNGVILVSRRPVIYECGPTCPCH
+ASCKNRVIQTGLKSRLEVFKTRNRGWGLRSWDSLRAGSFICEYAGEVKDNGNLRGNQEED
+AYVFDTSRVFNSFKWNYEPELVDEDPSTEVPEEFNLPSPLLISAKKFGNVARFMNHSCSP
+NVFWQPVIREGNGESVIHIAFFAMRHIPPMAELTYDYGISPTSEARDESLLHGQRTCLCG
+SEQCRGSFG
+>seq008
+MGSSHIPLDPSLNPSPSLIPKLEPVTESTQNLAFQLPNTNPQALISSAVSDFNEATDFSS
+DYNTVAESARSAFAQRLQRHDDVAVLDSLTGAIVPVEENPEPEPNPYSTSDSSPSVATQR
+PRPQPRSSELVRITDVGPESERQFREHVRKTRMIYDSLRMFLMMEEAKRNGVGGRRARAD
+GKAGKAGSMMRDCMLWMNRDKRIVGSIPGVQVGDIFFFRFELCVMGLHGHPQSGIDFLTG
+SLSSNGEPIATSVIVSGGYEDDDDQGDVIMYTGQGGQDRLGRQAEHQRLEGGNLAMERSM
+YYGIEVRVIRGLKYENEVSSRVYVYDGLFRIVDSWFDVGKSGFGVFKYRLERIEGQAEMG
+SSVLKFARTLKTNPLSVRPRGYINFDISNGKENVPVYLFNDIDSDQEPLYYEYLAQTSFP
+PGLFVQQSGNASGCDCVNGCGSGCLCEAKNSGEIAYDYNGTLIRQKPLIHECGSACQCPP
+SCRNRVTQKGLRNRLEVFRSLETGWGVRSLDVLHAGAFICEYAGVALTREQANILTMNGD
+TLVYPARFSSARWEDWGDLSQVLADFERPSYPDIPPVDFAMDVSKMRNVACYISHSTDPN
+VIVQFVLHDHNSLMFPRVMLFAAENIPPMTELSLDYGVVDDWNAKLAICN
+>seq009
+MDKSIPIKAIPVACVRPDLVDDVTKNTSTIPTMVSPVLTNMPSATSPLLMVPPLRTIWPS
+NKEWYDGDAGPSSTGPIKREASDNTNDTAHNTFAPPPEMVIPLITIRPSDDSSNYSCDAG
+AGPSTGPVKRGRGRPKGSKNSTPTEPKKPKVYDPNSLKVTSRGNFDSEITEAETETGNQE
+IVDSVMMRFDAVRRRLCQINHPEDILTTASGNCTKMGVKTNTRRRIGAVPGIHVGDIFYY
+WGEMCLVGLHKSNYGGIDFFTAAESAVEGHAAMCVVTAGQYDGETEGLDTLIYSGQGGTD
+VYGNARDQEMKGGNLALEASVSKGNDVRVVRGVIHPHENNQKIYIYDGMYLVSKFWTVTG
+KSGFKEFRFKLVRKPNQPPAYAIWKTVENLRNHDLIDSRQGFILEDLSFGAELLRVPLVN
+EVDEDDKTIPEDFDYIPSQCHSGMMTHEFHFDRQSLGCQNCRHQPCMHQNCTCVQRNGDL
+LPYHNNILVCRKPLIYECGGSCPCPDHCPTRLVQTGLKLHLEVFKTRNCGWGLRSWDPIR
+AGTFICEFAGLRKTKEEVEEDDDYLFDTSKIYQRFRWNYEPELLLEDSWEQVSEFINLPT
+QVLISAKEKGNVGRFMNHSCSPNVFWQPIEYENRGDVYLLIGLFAMKHIPPMTELTYDYG
+VSCVERSEEDEGFLVCPYLSSSLWPSSSEIHFLINSKGRAWYDKIYRKLASQGNVSSGLD
+SVKDEPEKLREEQMEGDGFKEKLSDSVLIDEKLEEYSDCDRTATTSRSHTDPVSSQSTHQ
+TPESFRTPITCDDDTFVSVSGISRDVSNLIPFATETPASPVQEKMANTRSFSNNSVKGNQ
+DEFFIEDFDVGPMDTIDLYDMTFREDPSDFDDNLLYAMRDRTKQLRSFKRKIMDAIKSKR
+RREKEYEQLAIWFGDADMGCDLVNDKEQSTTSIDSKSSQTNVPVVSEDSEWEIL
+>seq010
+MMMTQRISPSNKRRRVSFVRDFPQFSVKDESDIGGDDVATIKENLDGKEDSNCVGVAYRD
+HHRPKEESFDSIMKKAGFNVANGNLGNGKFPPSKRNVPLPCEGKVQPLSVEEGIKLMAYE
+SQRRRCFGKPLVSTKVVQKHRYSPAKKKLSNATALRVRHSPMKKLSNASRLRANAHRPTQ
+HKDERRSGVLSVIQRNRLSKDLTPRQKVQEVLRIFTLVFDELDRNKAARRGGSETAKSRI
+DYQTWTILREMGMQVNSQKRIGSVPGIKVGDKIQFKAALSVIGLHFGIMSGIDYMYKGNK
+EVATSIVSSEGNDYGDRFINDVMIYCGQGGNMRSKDHKAIKDQKLVGGNLALANSIKEKT
+PVRVIRGERRLDNRGKDYVYDGLYRVEKYWEERGPQGNILFKFKLRRTCQPYVDF
+>seq011
+MSQKRSLVFAIRDFPPGCGTHIDVSSSLNHPAEKAFKHPRTGDVSGENLSFAEAKPEGTC
+LKRESADQDHIFAAPEHNAKREPAGQDHVVAATTVAYATSSHRQKVEIGNSDCDPTPREK
+VLEVLSLFKQVYNQLDRDKKARRGGDFLDATSRIDLKTLTVLEKMGKQVNTEKRIGSVPG
+INIGDVFQYKTELRVVGLHSKPMCGIDYIKLGDDRITTSIVASEGYGYNDTYNSGVMVYT
+GEGGNVINKQKKTEDQKLVKGNLALATSMRQKSQVRVIRGEERLDRKGKRYVYDGLYMVE
+EYWVERDVRGKSVYKFKLCRIPGQLPLT
+>seq012
+MCLVGLHRNTAGGIDSLLAKESGVDGPAATSVVTSGKYDNETEDLETLIYSGHGGKPCDQ
+VLQRGNRALEASVRRRNEVRVIRGELYNNEKVYIYDGLYLVSDCWQVTGKSGFKEYRFKL
+LRKPGQPPGYAIWKLVENLRNHELIDPRQGFILGDLSFGEEGLRVPLVNEVDEEDKTIPD
+DFDYIRSQCYSGMTNDVNVDSQSLVQSYIHQNCTCILKNCGQLPYHDNILVCRKPLIYEC
+GGSCPTRMVETGLKLHLEVFKTSNCGWGLRSWDPIRAGTFICEFTGVSKTKEEVEEDDDY
+LFDTSRIYHSFRWNYEPELLCEDACEQVSEDANLPTQVLISAKEKGNVGRFMNHNCWPNV
+FWQPIEYDDNNGHIYVRIGLFAMKHIPPMTELTYDYGISCVEKTGEDEVIYKGKKICLCG
+SVKCRGSFG
+>seq013
+MGLVGLHSGTIDMEFIGVEDHGDEEGKQIAVSVISSGKNADKTEDPDSLIFTGFGGTDMY
+HGQPCNQKLERLNIPLEAAFRKKSIVRVVRCMKDEKRTNGNIYIYDGTYMITNRWEEEGQ
+NGFIVFKFKLVREPDQKPAFGIWKSIQNWRNGLSIRPGLILEDLSNGAENLKVCLVNEVD
+KENGPALFRYVTSLIHEVINNIPSMVDRCACGRRSCGSKHVFREKLSVSSSLVISAKKSG
+NVARFMNHSCSPNVFWQSIAREQNGLWCLYIGFFAMKHIPPLTELRYDYGKSRGGGKKMC
+LCRTKKCCGSFG
+>seq014
+MTRVNQLPCDCVSTAEESLTSGTCITPTHVTSLSSPLDRSGDVDPLPVSDESGGSKADES
+MTDADETKKRKRILSGDCEADENNKSDGEIASLNDGVDAFTAICEDLNCSLCNQLPDRPV
+TILCGHNFCLKCFDKWIDQGNQICATCRSTIPDKMAANPRVNSSLVSVIRYVKVAKTAGV
+GTANFFPFTSNQDGPENAFRTKRAKIGEENAARIYVTVPFDHFGPIPAEHDPVRNQGVLV
+GESWENRVECRQWGVHLPHVSCIAGQEDYGAQSVVISGGYKDDEDHGEWFLYTGRSRGRH
+FANEDQEFEDLNEALRVSCEMGYPVRVVRSYKDRYSAYAPKEGVRYDGVYRIEKCWRKAR
+FPVCRYLFVRCDNEPAPWNSDESGDRPRPLPNIPELETASDLFERKESPSWDFDEAEGRW
+RWMKPPPANHEQRERMKMAMTCLLLFVLIILVGSSSILYQY
+>seq015
+MTRVNQLPCDCVSTAEESLTSGTCITPTHVTSLSSPLDRSGDVDPLPVSDESGGSKADES
+MTDADETKKRKRILSGDCEADENNKSDGEIASLNDGVDAFTAICEDLNCSLCNQLPDRPV
+TILCGHNFCLKCFDKWIDQGNQICATCRSTIPDKMAANPRVNSSLVSVIRYVKVAKTAGV
+GTANFFPFTSNQDGPENAFRTKRAKIGEENAARIYVTVPFDHFGPIPAEHDPVRNQGVLV
+GESWENRVECRQWGVHLPHVSCIAGQEDYGAQSVVISGGYKDDEDHGEWFLYTGRRSYKD
+RYSAYAPKEGVRYDGVYRIEKCWRKARFPDSFKVCRYLFVRCDNEPAPWNSDESGDRPRP
+LPNIPELETASDLFERKESPSWDFDEAEGRWRWMKPPPANHEQRERMKMAMTCLLLFVLI
+ILVGSSSILYQY
+>seq016
+MAEQPRINSALVSVIRMAKVSKNANSAVSAAAYHYIRNDDRPDKAFTTERAKRAGKANAS
+SGQIFVTIPPDHFGPILAENDPKRSIGVLVGDTWEDRLECRQWGAHFPHVAGIAGQSTHG
+AQSVALSGGYVDDEDHGEWFLYTGSGGRDLSGNKRTNKEQSSDQKFEKLNAALRISCLKG
+YPVRVVRSHKEKRSSYAPEAGVRYDGVYRIEKCWRKISVQGKFKVCRYLFVRCDNEPAPW
+TSDIYGDRPRPLPKVDELKGATDISERKGTPSWDFDEKEGWKWVKPPPISRKPNLSGDPA
+TDKEIRRVARRAQMSVTERLLKEFGCSICKQVMKEPLTTPCAHNFCKLCLVGTYGSQSSM
+RERSRGGRTLRAQKIVKKCPSCPTDICDFLENPQINREMMDLIESLQRKAVEEGDTKTSS
+DVSNGAESSGDDGNNEALEKGEDDSSLKDDGSLKDDGKVVKAVVVIKEEDLQPKKSKGED
+EKEQGDKKMDSADVVDIAVEKKQATKRASEKAEKKQARKRKGDAVATNDGKRMKTGGDAM
+ETAAEEDAPLSGGTPVKRNSRKSSEVDAKGGGGSPVVSSPRRVTRSNAKASGEADGSPAT
+RTRRATRAEA
+>seq017
+MTPATQYPCDPEGVCMRCKSMPPPEESLTCGTCVTPWHVSCLLSPPETLSATLQWLCPDC
+SGETNPLPVSGVAAGYGSVGSDLVAAIHSIEADETLSAEEKAKKKQQLLSGKGVVDEDDE
+EEKKKTSKGKKPIDVLSHFECSFCMQSLQKPVSVRVLFALALMLVWFLESTPCGHNACLK
+CFLKWMGQGHRSCGTCRSVIPESMVTNPRINLSIVSAIRLARVSEKADARTSKVVHYVDN
+EDRPDKAFTTERAKKTGNANASSGKIFVTIPRDHFGPIPAENDPVRNQGLLVGESWKGRL
+ACRQWGAHFPHVSGIAGQASYGAQSVVLAGGYDDDEDHGEWFLYTGRTNTVQAFDQVFLN
+FNEALRLSCKLGYPVRVVRSTKDKRSPYAPQGGLLRYDGVYRIEKCWRIVGIQMCRFLFV
+RCDNEPAPWTSDEHGDRPRPLPNVPELNMATDLFERKESPSWDFDEGEDRWRWMKPPPAS
+KKAVKNVLDPEERKLLREAIKSANPNTMRARLLKEFKCQICQKVMTNPVTTPCAHNFCKA
+CLESKFAGTALVRERGSGGRKLRSQKSVMKCPCCPTDIAEFVQNPQVNREVAEVIEKLKK
+QEEEENAKSLDEGQCSGTSHEEEDDEQPKKRIKLDTDAEVSATVVESDMK
+>seq018
+MARDIQLPCDGDGVCMRCKSNPPPEESLTCGTCVTPWHVSCLSSPPKTLASTLQWHCPDC
+SGEIDPLPVSGGATGFESAGSDLVAAIRAIEADESLSTEEKAKMRQRLLSGKGVEEDDEE
+EKRKKKGKGKNPNLDVLSALGDNLMCSFCMQLPERPVTKPCGHNACLKCFEKWMGQGKRT
+CGKCRSIIPEKMAKNPRINSSLVAAIRLAKVSKSAAATTSKVFHFISNQDRPDKAFTTER
+AKKTGKANAASGKIYVTIPPDHFGPIPAENDPVRNQGLLVGESWEDRLECRQWGAHFPHV
+AGIAGQSTYGAQSVALSGGYKDDEDHGEWFLYTGSGGRDLSGNKRTNKEQSFDQKFEKSN
+AALKLSCKLGYPVRVVRSHKEKRSAYAPEEGVRYDGVYRIEKCWRKVGVQVCRYLFVRCD
+NEPAPWTSDENGDRPRPIPNIPELNMATDLFERKETPSWDFDEGEGCWKWMKPPPASKKS
+VNVLAPEERKNLRKAIKAAHSNTMRARLLKEFKCQICQQVLTLPVTTPCAHNFCKACLEA
+KFAGKTLVRERSTGGRTLRSRKNVLNCPCCPTDISDFLQNPQVNREVAEVIEKLKTQEED
+TAELEDEDEGECSGTTPEEDSEQPKKRIKLDTDATVSATIR
+>seq019
+MAIQTQLPCDGDGVCMRCQVTPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCS
+GVVVPSAAPGTGISGPESSGSVLVAAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDE
+EKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGKFF
+VTIPRDHFGPIPAANDVTRNQGVLVGESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVA
+LSGGYDDDEDHGEWFLYTGSGGRDLSGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRV
+VRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEH
+GDRPRPLPDVPELENATDLFVRKESPSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKR
+AKKGNNAMKARLLKEFSCQICRKVLSLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVR
+KLRAKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEAEVAESSNISEEEEEE
+SEPPTKKIKMDNNSVGDTSLSA
+>seq020
+MAIQTQLPCDGDGVCMRCQVNPPSEETLTCGTCVTPWHVSCLLPESLASSTGDWECPDCS
+GVVVPSAAPGTGISGPESSGSVLVTAIRAIQADVTLTEAEKAKKRQRLMSGGGDDGVDDE
+EKKKLEIFCSICIQLPERPVTTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSGEATAAKVHHIIRNQDRPDKAFTTERAVKTGKANAASGVLV
+GESWEDRQECRQWGVHFPHVAGIAGQAAVGAQSVALSGGYDDDEDHGEWFLYTGSGGRDL
+SGNKRVNKIQSSDQAFKNMNEALRLSCKMGYPVRVVRSWKEKRSAYAPAEGVRYDGVYRI
+EKCWSNVGVQGLHKMCRYLFVRCDNEPAPWTSDEHGDRPRPLPDVPELENATDLFVRKES
+PSWGFDEAEGRWKWMKSPPVSRMALDTEERKKNKRAKKGNNAMKARLLKEFSCQICRKVL
+SLPVTTPCAHNFCKACLEAKFAGITQLRDRSNGVRKLRAKKNIMTCPCCTTDLSEFLQNP
+QVNREMMEIIENFKKSEEEAEVAESSNISEEEGEEESEPPTKKIKMDKNSVGGTSLSA
+>seq021
+MAIETQLPCDGDGVCMRCQVNPPSEETLTCGTCVTPWHVPCLLPESLASSTGEWECPDCS
+GVVVPSAAPGTGNARPESSGSVLVAAIRAIQADETLTEAEKAKKRQKLMSGGGDDGVDEE
+EKKKLEIFCSICIQLPERPITTPCGHNFCLKCFEKWAVGQGKLTCMICRSKIPRHVAKNP
+RINLALVSAIRLANVTKCSVEATAAKVHHIIRNQDRPEKAFTTERAVKTGKANAASGKFF
+VTIPRDHFGPIPAENDVTRKQGVLVGESWEDRQECRQWGAHFPHIAGIAGQSAVGAQSVA
+LSGGYDDDEDHGEWFLYTGSGGRDLSGNKRINKKQSSDQAFKNMNESLRLSCKMGYPVRV
+VRSWKEKRSAYAPAEGVRYDGVYRIEKCWSNVGVQGSFKVCRYLFVRCDNEPAPWTSDEH
+GDRPRPLPNVPELETAADLFVRKESPSWDFDEAEGRWKWMKSPPVSRMALDPEERKKNKR
+AKNTMKARLLKEFSCQICREVLSLPVTTPCAHNFCKACLEAKFAGITQLRERSNGGRKLR
+AKKNIMTCPCCTTDLSEFLQNPQVNREMMEIIENFKKSEEEADASISEEEEEESEPPTKK
+IKMDNNSVGGSGTSLSA
+>seq022
+MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD
+YEVRLNDTIQLLVRQSLVLPHSTKERDSELSDTDSGCCLGQSESDKSSTHGEAAAETDSR
+PADEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEE
+DVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYD
+AEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
+SCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYC
+PECRNDASEVVLAGERLRESKKNAKMASATSSSQRDWGKGMACVGRTKECTIVPSNHYGP
+IPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGSYSLVLAGGYEDDVDHGNFFTYTG
+SGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVK
+GGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKK
+LGLTMQYPEGYLEALANREREKENSKREEEEQQEGGFASPRTGKGKWKRKSAGGGPSRAG
+SPRRTSKKTKVEPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEE
+TFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQT
+VLNQLFPGYGNGR
+>seq023
+MWIQVRTMDGKETHTVNSLSRLTKVQELRKKIEEVFHVEPQLQRLFYRGKQMEDGHTLFD
+YDVRLNDTIQLLVRQSLALPLSTKERDSELSDSDSGYGVGHSESDKSSTHGEGAAEADDK
+TVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDIMY
+HVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQVVMANYNVDYPRKRGFWYDVEIC
+RKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNT
+GKSGPSCRFCKDDENKPCRKCACHVCGGREAPEKQLLCDECDMAFHLYCLKPPLTSVPPE
+PEWYCPSCRTDSSEVVQAGEKLKESKKKAKMASATSSSRRDWGKGMACVGRTTECTIVPA
+NHFGPIPGVPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDNGNY
+FTYTGSGGRDLSGNKRTAGQSSDQKLTNNNRALALNCHSPINEKGAEAEDWRQGKPVRVV
+RNMKGGKHSKYAPAEGNRYDGIYKVVKYWPERGKSGFLVWRYLLRRDDTEPEPWTREGKD
+RTRQLGLTMQYPEGYLEALANKEKSRKRPAKALEQGPSSSKTGKSKQKSTGPTLSSPRAS
+KKSKLEPYTLSEQQANLIKEDKGNAKLWDDVLTSLQDGPYQIFLSKVKEAFQCICCQELV
+FRPVTTVCQHNVCKDCLDRSFRAQVFSCPACRFELDHSSPTRVNQPLQTILNQLFPGYGS
+GR

tests/data/fastq/methylated_dna/bisulfite-seq_test_data.md

@@ -0,0 +1,60 @@
+# E. coli paired-end test dataset for Bisulfite-seq applications
+
+The E. coli data set was generated using [Sherman](https://github.com/FelixKrueger/Sherman) as 10,000 reads of paired-end data, with average methylation levels of 80% in CpG context, and 10% in non-CG context. The files can be found in the folder: genaral/fastq/dna, and are called:
+
+
+`Ecoli_10K_methylated_R1.fastq.gz`
+
+`Ecoli_10K_methylated_R2.fastq.gz`
+
+```bash
+Sherman --non_dir --genome /bi/scratch/Genomes/E_coli/ --paired -n 10000 -l 100 --CG 20 --CH 90
+```
+
+The data is non-directional, so it should produce roughly 25% mapping to each of the `OT`, `CTOT`, `CTOB` and `OB` strands. Thus, the data can be used for bisulfite mapping in standard (= directional), `--pbat` and `--non_directional` mode.
+
+A test alignment should look roughly like this:
+
+`bismark --genome /bi/scratch/Genomes/E_coli/ -1 Ecoli_10K_methylated_R1.fastq.gz -2 Ecoli_10K_methylated_R2.fastq.gz --non_dir`
+
+``` csv
+Bismark report for: Ecoli_10K_methylated_R1.fastq.gz and Ecoli_10K_methylated_R2.fastq.gz (version: v0.22.3)
+Bismark was run with Bowtie 2 against the bisulfite genome of /bi/scratch/Genomes/E_coli/ with the specified options: -q --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
+Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)
+
+Final Alignment report
+======================
+Sequence pairs analysed in total:       10000
+Number of paired-end alignments with a unique best hit: 9320
+Mapping efficiency:     93.2%
+Sequence pairs with no alignments under any condition:  0
+Sequence pairs did not map uniquely:    680
+Sequence pairs which were discarded because genomic sequence could not be extracted:    0
+
+Number of sequence pairs with unique best (first) alignment came from the bowtie output:
+CT/GA/CT:       2341    ((converted) top strand)
+GA/CT/CT:       2329    (complementary to (converted) top strand)
+GA/CT/GA:       2356    (complementary to (converted) bottom strand)
+CT/GA/GA:       2294    ((converted) bottom strand)
+
+Final Cytosine Methylation Report
+=================================
+Total number of C's analysed:   471997
+
+Total methylated C's in CpG context:    111011
+Total methylated C's in CHG context:    11923
+Total methylated C's in CHH context:    21433
+Total methylated C's in Unknown context:        0
+
+Total unmethylated C's in CpG context:  27790
+Total unmethylated C's in CHG context:  105877
+Total unmethylated C's in CHH context:  193963
+Total unmethylated C's in Unknown context:      0
+
+C methylated in CpG context:    80.0%
+C methylated in CHG context:    10.1%
+C methylated in CHH context:    10.0%
+Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0
+
+Bismark completed in 0d 0h 0m 12s
+```

tests/data/fastq/rna/paired_end_RNAseq_test_data.md

@@ -0,0 +1,7 @@
+# Paired-end RNA-seq test dataset
+
+The data here are 2x 76bp RNA-seq data from mouse (10,000 reads of paired-end data). The files can be found in the folder: genaral/fastq/rna, and are called:
+
+`test_R1.fastq.gz`
+
+`test_R2.fastq.gz`