diff --git a/.gitignore b/.gitignore
index 0fb699fd11be7d4e2a8592eca29810dcb58dce5e..bdd964eeb27c113b8901b921510456b33c8bf60d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,4 @@
*_transfer_info_file.sh
*.o[1-9]*
+*.nextflow*
+work
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..6ed459d7b786ecb8deb098b4a0053547afa6a9af
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,6 @@
+test:
+ script:
+ - conda env create -p $PWD/conda
+ - conda activate $PWD/conda
+ - cd tests/ && ./run_tests.sh
+ - conda deactivate
diff --git a/README.md b/README.md
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..dcd54f8645b26b0e7d7dc0e7337102b3c4a28376 100644
--- a/README.md
+++ b/README.md
@@ -0,0 +1,62 @@
+# Trio-Whole-Exome pipeline
+
+This is an automated version of the scripts currently run manually according to SOP as part of the whole exome trios
+project with David Fitzpatrick's group. This pipeline is controlled by [NextFlow](https://www.nextflow.io/)
+
+
+## Setup
+
+A [Conda](https://docs.conda.io) environment containing NextFlow is available in `environment.yaml`. Once you have Conda
+installed, you can create an environment by `cd`-ing into this project and running the command:
+
+ $ conda env create -n <environment_name>
+
+
+## Running
+
+The pipeline requires two main input files:
+
+### Samplesheet
+
+This is a tab-separated file mapping fastq pairs to metadata. The columns are individual ID, family ID, fastq sample ID,
+r1 fastq and r2 fastq. If a sample has been sequenced over multiple lanes, then include a line for each fastq pair:
+
+ individual_id family_id sample_id read_1 read_2
+ 000001 000001 12345_000001_000001_WESTwist_IDT-B path/to/lane_1_r1.fastq.gz path/to/lane_1_r2.fastq.gz
+ 000001 000001 12345_000001_000001_WESTwist_IDT-B path/to/lane_2_r1.fastq.gz path/to/lane_2_r2.fastq.gz
+
+###Â Ped file
+
+Tab-separated Ped file mapping individuals to each other and affected status. Per the
+[specification](https://gatk.broadinstitute.org/hc/en-us/articles/360035531972-PED-Pedigree-format), the columns are
+family ID, individual ID, father ID, mother ID, sex (1=male, 2=female, other=unknown), affected status (-9 or 0=missing,
+1=unaffected, 2=affected):
+
+ 000001 000001 000002 000003 2 2
+ 000001 000002 0 0 1 1
+ 000001 000003 0 0 2 1
+
+The pipeline can now be run. First, check for errors:
+
+ $ nextflow run pipeline/validation.nf --ped_file path/to/batch.ped --sample_sheet path/to/batch_samplesheet.tsv
+
+Todo: run the main processing
+
+## Tests
+
+This pipeline has automated tests contained in the folder `tests/`. To the run the tests locally, `cd` to this folder
+with your Conda environment active and run `./run_tests.sh`.
+
+
+## Terminology
+
+- Batch: slightly ambiguous term - could be a pipeline batch, a sequencing batch or a BCBio batch
+ - Pipeline batch: a single run of this pipeline, potentially mixing samples and families from multiple
+ sequencing batches
+ - Sequencing batch: a group of samples that were prepared and sequenced together
+ - BCBio batch: used internally by BCBio to identify a family
+- Sample ID: specific to a sequencing batch, family ID, individual ID and extraction kit type
+- file_list.tsv: there's one of these files per sequencing batch, summarising all fastqs in the batch. A
+ pipeline batch may need to refer to multiple different individuals across different file lists.
+- Ped file: defines family relationships between individuals. There's always one Ped file per pipeline batch.
+- Sample sheet: links the Ped file and file list(s) by defining what raw fastqs belong to each individual.
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4ba44ad377ef4aac7b867514c39ae8040b61d813
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,12 @@
+---
+
+channels:
+ - conda-forge
+ - bioconda
+ - defaults
+
+dependencies:
+ - coreutils=8.25 # gives us cross-platform md5sum
+ - python=3.9
+ - nextflow=21.04.0
+# - bcbio-nextgen=1.2.8
diff --git a/pipeline/inputs.nf b/pipeline/inputs.nf
new file mode 100644
index 0000000000000000000000000000000000000000..e5f6b319bb2e539b4b7ee554d02ed554b8917e26
--- /dev/null
+++ b/pipeline/inputs.nf
@@ -0,0 +1,94 @@
+nextflow.enable.dsl = 2
+
+params.ped_file = null
+params.sample_sheet = null
+
+workflow read_inputs {
+ /*
+ Read the input files into channels. This has to be a workflow so the channels
+ can be included in other scripts
+ */
+
+ main:
+ /*
+ ch_family_info - tuple channel of family members:
+ [
+ [
+ family: family1,
+ indv: indv1,
+ father: indv2,
+ mother: indv3,
+ sex: 2,
+ affected: 2
+ ],
+ ...
+ ]
+ */
+ ped_file = file(params.ped_file, checkIfExists: true)
+ ch_ped_file_info = Channel.fromPath(ped_file)
+ .splitCsv(sep: '\t')
+ .map(
+ { line ->
+ [
+ line[1], // indv ID
+ line[0], // family ID
+ line[2], // father
+ line[3], // mother
+ line[4], // sex
+ line[5] // affected
+ ]
+ }
+ )
+
+
+ /*
+ ch_samplesheet_info - Tuple channel of individual ID, r1 fastqs and r2 fastqs:
+ [
+ [
+ indv1,
+ [/abs/path/to/lane_1_r1.fastq.gz, /abs/path/to/lane_2_r1.fastq.gz],
+ [/abs/path/to/lane_1_r2.fastq.gz, /abs/path/to/lane_2_r2.fastq.gz]
+ ],
+ [
+ indv2,
+ ...
+ ]
+ ]
+ */
+ samplesheet = file(params.sample_sheet, checkIfExists: true)
+ ch_samplesheet_info = Channel.fromPath(samplesheet)
+ .splitCsv(sep:'\t', header: true)
+ .map(
+ { line -> [line.individual_id, file(line.read_1), file(line.read_2)] }
+ )
+ .groupTuple()
+
+ /*
+ ch_individuals_by_family - merge of samplesheet and ped file information,
+ grouped by family ID:
+ [
+ [
+ indv1,
+ [
+ indv_id,
+ family_id,
+ father_id,
+ mother_id,
+ sex,
+ affected,
+ r1_fastqs,
+ r2_fastqs
+ ]
+ ],
+ ...
+ ]
+ */
+ ch_individuals_by_family = ch_ped_file_info
+ .join(ch_samplesheet_info)
+ .map({[it[1], it]})
+
+ emit:
+ ch_samplesheet_info
+ ch_ped_file_info
+ ch_individuals_by_family
+}
diff --git a/pipeline/lib/PipelineException.groovy b/pipeline/lib/PipelineException.groovy
new file mode 100644
index 0000000000000000000000000000000000000000..8a3c4fbf6730f59156f6db02b3876ad29010885e
--- /dev/null
+++ b/pipeline/lib/PipelineException.groovy
@@ -0,0 +1,12 @@
+import org.codehaus.groovy.GroovyException
+
+class PipelineException extends GroovyException {
+ /*
+ Simple exception class that can be thrown at pipeline runtime.
+ Maybe there's a better way of raising errors?
+ */
+ public PipelineException(String message) {
+ super(message)
+ }
+
+}
diff --git a/pipeline/main.nf b/pipeline/main.nf
new file mode 100644
index 0000000000000000000000000000000000000000..2fb6521d9c1c76e7e23338b68f4c5e044ae709fa
--- /dev/null
+++ b/pipeline/main.nf
@@ -0,0 +1,128 @@
+nextflow.enable.dsl = 2
+
+include {read_inputs} from './inputs.nf'
+include {validation} from './validation.nf'
+
+params.bcbio = null
+params.bcbio_template = null
+
+process merge_fastqs {
+ publishDir "outputs/individuals/$indv_id/merged_fastqs", mode: 'copy'
+
+ input:
+ tuple(val(indv_id), path(r1), path(r2))
+
+ output:
+ tuple(
+ val(indv_id),
+ path("${indv_id}_merged_r1.fastq.gz"),
+ path("${indv_id}_merged_r2.fastq.gz")
+ )
+
+ script:
+ // todo: pigz if gzip becomes a bottleneck
+ """
+ cat ${r1.join(' ')} | gzip -c > ${indv_id}_merged_r1.fastq.gz &
+ cat ${r2.join(' ')} | gzip -c > ${indv_id}_merged_r2.fastq.gz
+ """
+}
+
+process write_bcbio_csv {
+ publishDir "outputs/families/$family_id", mode: 'copy'
+
+ input:
+ tuple(val(family_id), val(individual_info))
+
+ output:
+ path("${family_id}.csv")
+
+ script:
+ """
+ #!/usr/bin/env python
+
+ individual_info = '$individual_info'
+ lines = individual_info.lstrip('[').rstrip(']').split('], [')
+
+ with open('${family_id}.csv', 'w') as f:
+ f.write('samplename,description,batch,sex,phenotype,variant_regions\\n')
+ for l in lines:
+ l = l.lstrip('[').rstrip(']').split(', ')
+ f.write(','.join(l))
+ f.write('\\n')
+ """
+}
+
+
+process prepare_bcbio_yaml {
+ publishDir "outputs/families/$family_id", mode: 'copy'
+
+ input:
+ tuple(val(family_id), val(family_fastqs))
+ val(family_csv)
+
+ output:
+ path("${family_id}.yaml")
+
+ script:
+ """
+ ${params.bcbio_prepare_samples} --out . --csv $family_csv
+
+ ${params.bcbio} -w template ${params.bcbio_template} ${family_id}-merged.csv ${family_fastqs.join(' ')}
+ """
+}
+
+process run_bcbio {
+ input:
+ path(bcbio_config)
+
+ script:
+ """
+ ${params.bcbio} $bcbio_config -n 16 -t local
+ """
+
+}
+
+workflow prepare_bcbio_config {
+ /*
+ - For each individual, merge all R1 and R2 fastqs
+ - For each family:
+ - Read the relevant information from the samplesheet, ped files and merged fastqs
+ - Write a BCBio config file
+ - Run BCBio on it
+ */
+
+ take:
+ ch_samplesheet_info
+ ch_individuals_by_family
+
+ main:
+ ch_merged_fastqs = merge_fastqs(ch_samplesheet_info)
+ ch_joined_family_info = ch_individuals_by_family.map({ k, v -> v })
+ .join(ch_merged_fastqs)
+
+ ch_metadata = ch_joined_family_info.map(
+ { sample_id, family_id, father, mother, sex, phenotype, r1s, r2s, merged_r1, merged_r2 ->
+ [family_id, [sample_id, father, mother, sex, phenotype, merged_r1, merged_r2]]
+ }).groupTuple()
+
+ ch_family_fastqs = ch_joined_family_info.map(
+ { sample_id, family_id, father, mother, sex, phenotype, r1s, r2s, merged_r1, merged_r2 ->
+ [family_id, merged_r1, merged_r2]
+ }
+ ).groupTuple()
+
+ ch_bcbio_csv = write_bcbio_csv(ch_metadata)
+ ch_bcbio_yaml = prepare_bcbio_yaml(ch_family_fastqs, ch_bcbio_csv)
+ run_bcbio(ch_bcbio_yaml)
+}
+
+
+workflow {
+ read_inputs()
+ ch_samplesheet_info = read_inputs.out[0]
+ ch_ped_file_info = read_inputs.out[1]
+ ch_individuals_by_family = read_inputs.out[2]
+
+ validation(ch_samplesheet_info)
+ prepare_bcbio_config(ch_samplesheet_info, ch_individuals_by_family)
+}
diff --git a/pipeline/validation.nf b/pipeline/validation.nf
new file mode 100644
index 0000000000000000000000000000000000000000..ba6c2295dc2372e86f2abd9b5f5aed37486d88ab
--- /dev/null
+++ b/pipeline/validation.nf
@@ -0,0 +1,41 @@
+nextflow.enable.dsl = 2
+
+include {read_inputs} from './inputs.nf'
+
+process check_md5s {
+ input:
+ val(md5sum_file)
+
+ script:
+ """
+ # I don't understand why getParent works since md5sum_file is not a path, but it works
+ cd ${md5sum_file.getParent()}
+ md5sum -c ${md5sum_file.getName()}
+ """
+}
+
+workflow validation {
+ /*
+ Take a parsed samplesheet, flatten it and parse into a channel of observed vs.
+ expected checksums. Calls check_errors above to raise an exception upon any
+ mismatches.
+ */
+
+ take:
+ ch_samplesheet_info
+
+ main:
+ ch_fastqs = ch_samplesheet_info
+ .map(
+ { indv, r1, r2 ->
+ [r1, r2]
+ }
+ ).flatten()
+ .map({file(it)})
+
+ ch_md5_files = ch_fastqs.map(
+ { fastq -> fastq.getParent().getParent() + '/md5sums.txt' }
+ ).unique()
+
+ check_md5s(ch_md5_files)
+}
diff --git a/tests/.gitignore b/tests/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..b25c15b81fae06e1c55946ac6270bfdb293870e8
--- /dev/null
+++ b/tests/.gitignore
@@ -0,0 +1 @@
+*~
diff --git a/tests/assets/bcbio/bcbio_template.yaml b/tests/assets/bcbio/bcbio_template.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..c0dad7fbc7e8c7ededcf3f67236a4d79495468ad
--- /dev/null
+++ b/tests/assets/bcbio/bcbio_template.yaml
@@ -0,0 +1,22 @@
+details:
+- algorithm:
+ platform: illumina
+ quality_format: standard
+ aligner: bwa
+ align_split_size: false
+ trim_reads: fastp
+ adapters: [nextera2, polyg]
+ mark_duplicates: true
+ realign: false
+ recalibrate: true
+ effects: vep
+ effects_transcripts: all
+ variantcaller: gatk-haplotype
+ indelcaller: false
+ remove_lcr: true
+ tools_on:
+ - vep_splicesite_annotations
+ analysis: variant2
+ genome_build: hg38
+upload:
+ dir: outputs/bcbio/results
diff --git a/tests/assets/input_data/.gitignore b/tests/assets/input_data/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..04bd712af1e74dc477ce6fef6b699f9e10b0f2b0
--- /dev/null
+++ b/tests/assets/input_data/.gitignore
@@ -0,0 +1 @@
+giab
diff --git a/tests/assets/input_data/Readme.md b/tests/assets/input_data/Readme.md
new file mode 100644
index 0000000000000000000000000000000000000000..84e19dfad517cbf1949328686f6e68010ced7eeb
--- /dev/null
+++ b/tests/assets/input_data/Readme.md
@@ -0,0 +1,15 @@
+# Test input data
+
+The test data here consists of:
+
+## Edinburgh Genomics test data
+
+Family 000001 - an example of a complete trio. Individuals: 000001, 000002, 000003
+Family 000002 - an incomplete trio with only one parent. Individuals: 000004, 000005
+Family 000003 - a singleton test case for an unexpected MD5 checksum. Individuals: 000006
+
+Todo: more EG test data from a different download date - maybe a singleton, complete duo and a quad
+
+## CRF
+
+todo: CRF test data
diff --git a/tests/assets/input_data/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed b/tests/assets/input_data/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
new file mode 100644
index 0000000000000000000000000000000000000000..c62b674f3fc8f328dcfcc4903eaa5cbcc5d63c6d
--- /dev/null
+++ b/tests/assets/input_data/Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
@@ -0,0 +1,215004 @@
+chr1 65549 65588
+chr1 69021 70023
+chr1 182693 182761
+chr1 183098 183255
+chr1 183906 184173
+chr1 450724 451693
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diff --git a/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_1.fastq.gz b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.count b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.count
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.gz b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/file_list.tsv b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/file_list.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..b91c6b686fd3587546f8122c6e66228be20eea0b
--- /dev/null
+++ b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/file_list.tsv
@@ -0,0 +1,21 @@
+File Run_ID Lane_or_Cell Read Read_length_BP Total_reads Barcode_sequence Sample_name Library_ID File_size Platform Model
+12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 1 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000001_000001_WESTwist_IDT-B 00001AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 1 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000001_000001_WESTwist_IDT-B 00001AM0001L01 500.2M Illumina NovaSeq 6000
+12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 2 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000001_000001_WESTwist_IDT-B 00001AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 2 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000001_000001_WESTwist_IDT-B 00001AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 3 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000002_000001_WESTwist_IDT-B 00002AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 3 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000002_000001_WESTwist_IDT-B 00002AM0001L01 500.2M Illumina NovaSeq 6000
+12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 4 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000002_000001_WESTwist_IDT-B 00002AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 4 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000002_000001_WESTwist_IDT-B 00002AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 5 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000003_000001_WESTwist_IDT-B 00003AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 5 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000003_000001_WESTwist_IDT-B 00003AM0001L01 500.2M Illumina NovaSeq 6000
+12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 6 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000003_000001_WESTwist_IDT-B 00003AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 6 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000003_000001_WESTwist_IDT-B 00003AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 7 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000004_000002_WESTwist_IDT-B 00004AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 7 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000004_000002_WESTwist_IDT-B 00004AM0001L01 500.2M Illumina NovaSeq 6000
+12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.gz 200922_A00001_0001_BHNTGMDMXX 8 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000004_000002_WESTwist_IDT-B 00004AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.gz 200922_A00001_0001_BHNTGMDMXX 8 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000004_000002_WESTwist_IDT-B 00004AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_1.fastq.gz 200923_A00001_0002_BRLSHNMKBX 1 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000005_000002_WESTwist_IDT-B 00005AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_1_00005AM0001L01_2.fastq.gz 200923_A00001_0002_BRLSHNMKBX 1 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000005_000002_WESTwist_IDT-B 00005AM0001L01 500.2M Illumina NovaSeq 6000
+12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_1.fastq.gz 200923_A00001_0002_BRLSHNMKBX 2 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000005_000002_WESTwist_IDT-B 00005AM0001L01 500.1M Illumina NovaSeq 6000
+12345_000005_000002_WESTwist_IDT-B/200923_A00001_0002_BRLSHNMKBX_2_00005AM0001L01_2.fastq.gz 200923_A00001_0002_BRLSHNMKBX 2 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12345_000005_000002_WESTwist_IDT-B 00005AM0001L01 500.1M Illumina NovaSeq 6000
diff --git a/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/md5sums.txt b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/md5sums.txt
new file mode 100644
index 0000000000000000000000000000000000000000..25e1b82de4ce7cfd878dbb3b55ff01c3754ebca9
--- /dev/null
+++ b/tests/assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/md5sums.txt
@@ -0,0 +1,32 @@
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_7_00004AM0001L01_2.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_1.fastq.gz
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.count
+d41d8cd98f00b204e9800998ecf8427e 12345_000004_000002_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_8_00004AM0001L01_2.fastq.gz
diff --git a/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_1.fastq.gz b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_1.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_2.fastq.gz b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_2.fastq.gz
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/file_list.tsv b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/file_list.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..d347008b364719d07d5294d15a6bf2289ec4fdc4
--- /dev/null
+++ b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/file_list.tsv
@@ -0,0 +1,3 @@
+File Run_ID Lane_or_Cell Read Read_length_BP Total_reads Barcode_sequence Sample_name Library_ID File_size Platform Model
+12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_1.fastq.gz 211005_A00002_0002_AJTHSNRLXX 1 1 100 12345167 GTGACGGAGC+TGGCGGTCCA 12346_000006_000003_WESTwist_IDT-B 00002AM0002L01 500.1M Illumina NovaSeq 6000
+12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_2.fastq.gz 211005_A00002_0002_AJTHSNRLXX 1 2 100 12345167 GTGACGGAGC+TGGCGGTCCA 12346_000006_000003_WESTwist_IDT-B 00002AM0002L01 500.1M Illumina NovaSeq 6000
diff --git a/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/md5sums.txt b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/md5sums.txt
new file mode 100644
index 0000000000000000000000000000000000000000..029d28408bb0eb60ca876f986228280359ee87f2
--- /dev/null
+++ b/tests/assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/md5sums.txt
@@ -0,0 +1,2 @@
+0123456789abcdef0123456789abcdef 12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_1.fastq.gz
+0123456789abcdef0123456789abcdef 12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_2.fastq.gz
diff --git a/tests/assets/input_data/ped_files/batch_1.ped b/tests/assets/input_data/ped_files/batch_1.ped
new file mode 100644
index 0000000000000000000000000000000000000000..b494a07f123e08320cabb914cd6e47afd1ba6fc7
--- /dev/null
+++ b/tests/assets/input_data/ped_files/batch_1.ped
@@ -0,0 +1,6 @@
+000001 000001 000002 000003 2 2
+000001 000002 0 0 1 1
+000001 000003 0 0 2 1
+000002 000004 000005 000006 2 2
+000002 000005 0 0 1 1
+000002 000006 0 0 2 1
diff --git a/tests/assets/input_data/ped_files/batch_2_md5_errors.ped b/tests/assets/input_data/ped_files/batch_2_md5_errors.ped
new file mode 100644
index 0000000000000000000000000000000000000000..2f7610f78a4b99d1a587df4dfbceb67ae47abeb5
--- /dev/null
+++ b/tests/assets/input_data/ped_files/batch_2_md5_errors.ped
@@ -0,0 +1 @@
+000003 000006 0 0 1 1
diff --git a/tests/assets/input_data/sample_sheets/batch_1.tsv b/tests/assets/input_data/sample_sheets/batch_1.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..7b93d5429ffa4c848dc5cf1898017b33d097e7ea
--- /dev/null
+++ b/tests/assets/input_data/sample_sheets/batch_1.tsv
@@ -0,0 +1,7 @@
+individual_id family_id sample_id read_1 read_2
+000001 000001 12345_000001_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_1_00001AM0001L01_2.fastq.gz
+000001 000001 12345_000001_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000001_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_2_00001AM0001L01_2.fastq.gz
+000002 000001 12345_000002_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_3_00002AM0001L01_2.fastq.gz
+000002 000001 12345_000002_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000002_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_4_00002AM0001L01_2.fastq.gz
+000003 000001 12345_000003_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_5_00003AM0001L01_2.fastq.gz
+000003 000001 12345_000003_000001_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12345_A_Researcher/20210922/12345_000003_000001_WESTwist_IDT-B/200922_A00001_0001_BHNTGMDMXX_6_00003AM0001L01_2.fastq.gz
diff --git a/tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv b/tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..fca9441691e9a6c36644bc0960382b31e71fff22
--- /dev/null
+++ b/tests/assets/input_data/sample_sheets/batch_2_md5_errors.tsv
@@ -0,0 +1,2 @@
+individual_id family_id sample_id read_1 read_2
+000006 000003 12346_000006_000003_WESTwist_IDT-B assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_1.fastq.gz assets/input_data/edinburgh_genomics/X12346_MD5_Errors/20211005/12346_000006_000003_WESTwist_IDT-B/211005_A00002_0002_AJTHSNRLXX_1_00002AM0002L01_2.fastq.gz
diff --git a/tests/assets/input_data/scripts/giab.sh b/tests/assets/input_data/scripts/giab.sh
new file mode 100755
index 0000000000000000000000000000000000000000..3a8b9fbf4e91318929ab851c4c09917c3449b8f6
--- /dev/null
+++ b/tests/assets/input_data/scripts/giab.sh
@@ -0,0 +1,154 @@
+#!/bin/bash
+#
+# Downloads whole genome data from Genome in a Bottle (https://github.com/genome-in-a-bottle/giab_data_indexes) for two trios.
+# Extracts the FASTQ reads for each of these trios overlapping the TWIST exome targets for chr22 only.
+#
+# Requires:
+# samtools
+# bedtools
+# bazam
+
+TWIST_TARGET=Twist_Exome_RefSeq_targets_hg38.plus15bp.bed
+
+###
+# Prepare the chr22 target subset
+###
+mkdir -p giab
+cd giab
+echo "chr22 0 50818468" > chr22.bed
+perl -pi -e 's/ /\t/g' chr22.bed
+bedtools intersect -a chr22.bed -b ../$TWIST_TARGET > TWIST.chr22.bed
+sed -e 's/chr//' TWIST.chr22.bed > TWIST.22.bed
+
+###
+# AshkenazimTrio: Illumina whole exome (for testing this script)
+##
+
+# Fetch the index
+mkdir -p raw_data/AshkenazimTrioExome
+cd raw_data/AshkenazimTrioExome
+wget https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/alignment.index.AJtrio_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015
+index=alignment.index.AJtrio_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015
+
+for ((i = 2; i <= 4; i = i + 1))
+do
+ # Download the BAM and its md5 checksum
+ bam=`head -n $i $index | tail -n 1 | cut -f 1`
+ bam_md5=`head -n $i $index | tail -n 1 | cut -f 2`
+
+ bam_base=`basename $bam`
+
+ # Validate the md5 checksum
+ echo $bam_md5 $bam_base > $bam_base.md5
+ wget $bam
+ md5sum --check $bam_base.md5
+
+ # Freshly index
+ samtools index $bam_base
+
+ # Extract FASTQ
+ java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+
+ # Gzip the FASTQ reads
+ gzip *.fastq
+
+ # Subset to 10K reads per sample
+ sample=`echo $bam_base | cut -f 6 -d '_'`
+ seqtk sample -s 100 ${bam_base%.bam}_R1.fastq.gz 10000 > ${sample}_R1.fastq.gz
+ seqtk sample -s 100 ${bam_base%.bam}_R2.fastq.gz 10000 > ${sample}_R2.fastq.gz
+
+ # Move to output
+ mkdir -p ../../AshkenazimTrioExome
+ mv ${sample}_R{1,2}.fastq.gz ../../AshkenazimTrioExome
+done
+
+# Move back up to giab working folder
+cd ../..
+
+###
+# AshkenazimTrio:
+###
+mkdir -p raw_data/AshkenazimTrio
+cd raw_data/AshkenazimTrio
+wget https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/alignment.index.AJtrio_Illumina_2x250bps_novoalign_GRCh37_GRCh38_NHGRI_06062016
+index=alignment.index.AJtrio_Illumina_2x250bps_novoalign_GRCh37_GRCh38_NHGRI_06062016
+
+for ((i = 2; i <= 6; i = i + 2))
+do
+ # Download the BAM and its md5 checksum
+ bam=`head -n $i $index | tail -n 1 | cut -f 1`
+ bam_md5=`head -n $i $index | tail -n 1 | cut -f 2`
+
+ bam_base=`basename $bam`
+
+ # Validate the md5 checksum
+ echo $bam_md5 $bam_base > $bam_base.md5
+ wget $bam
+ md5sum --check $bam_base.md5
+
+ # Freshly index
+ samtools index $bam_base
+
+ # Extract FASTQ
+ java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+
+ # Gzip the FASTQ reads
+ gzip *.fastq
+
+ # Subset to 10K reads per sample
+ sample=`echo $bam_base | cut -f 1 -d '.'`
+ seqtk sample -s 100 ${bam_base%.bam}_R1.fastq.gz 10000 > ${sample}_R1.fastq.gz
+ seqtk sample -s 100 ${bam_base%.bam}_R2.fastq.gz 10000 > ${sample}_R2.fastq.gz
+
+ # Move to output folder
+ mkdir -p ../../AshkenazimTrio
+ mv ${sample}_R{1,2}.fastq.gz ../../AshkenazimTrio
+done
+
+# Move back up to giab working folder
+cd ../..
+
+###
+# ChineseTrio: Illumina WGS 2x250bp 300X for son; 2x150bp 100x for parents (GRCh38)
+###
+
+# Fetch the index
+mkdir -p raw_data/ChineseTrio
+cd raw_data/ChineseTrio
+wget https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/ChineseTrio/alignment.index.ChineseTrio_Illumina300X100X_wgs_novoalign_GRCh37_GRCh38_NHGRI_04062016
+index=alignment.index.ChineseTrio_Illumina300X100X_wgs_novoalign_GRCh37_GRCh38_NHGRI_04062016
+
+for ((i = 2; i <= 6; i = i + 2))
+do
+ # Download the BAM and its md5 checksum
+ bam=`head -n $i $index | tail -n 1 | cut -f 1`
+ bam_md5=`head -n $i $index | tail -n 1 | cut -f 2`
+
+ bam_base=`basename $bam`
+
+ # Validate the md5 checksum
+ echo $bam_md5 $bam_base > $bam_base.md5
+ wget $bam
+ md5sum --check $bam_base.md5
+
+ # Freshly index
+ samtools index $bam_base
+
+ # Extract FASTQ
+ java -jar ../../../../../software/bazam.jar -bam $bam_base -L ../../TWIST.22.bed -r1 ${bam_base%.bam}_R1.fastq -r2 ${bam_base%.bam}_R2.fastq
+
+ # Gzip the FASTQ reads
+ gzip *.fastq
+
+ # Subset to 10K reads per sample
+ sample=`echo $bam_base | cut -f 1 -d '.'`
+ seqtk sample -s 100 ${bam_base%.bam}_R1.fastq.gz 10000 > ${sample}_R1.fastq.gz
+ seqtk sample -s 100 ${bam_base%.bam}_R2.fastq.gz 10000 > ${sample}_R2.fastq.gz
+
+ # Move to output folder
+ mkdir -p ../../ChineseTrio
+ mv ${sample}_R{1,2}.fastq.gz ../../ChineseTrio
+done
+
+# Move back up to enclosing folder
+cd ../../..
diff --git a/tests/run_tests.sh b/tests/run_tests.sh
new file mode 100755
index 0000000000000000000000000000000000000000..2ae8c81c5b292d605b782e5edd2277bc7aca3cf7
--- /dev/null
+++ b/tests/run_tests.sh
@@ -0,0 +1,38 @@
+#!/bin/bash
+
+source scripts/test_config.sh
+bcbio=$PWD/scripts/bcbio_nextgen.py
+bcbio_prepare_samples=$PWD/scripts/bcbio_prepare_samples.py
+
+common_args="--bcbio $bcbio --bcbio_prepare_samples $bcbio_prepare_samples --bcbio_template $PWD/bcbio/bcbio_template.yaml"
+
+test_exit_status=0
+
+nextflow clean -f
+rm -r ./outputs/* ./work/*
+
+echo "Test case 1: simple trio"
+run_nextflow ../pipeline/main.nf --ped_file assets/input_data/ped_files/batch_1.ped --sample_sheet assets/input_data/sample_sheets/batch_1.tsv $common_args
+test_exit_status=$(( $test_exit_status + $? ))
+for f in "
+ outputs/individuals/000001/merged_fastqs/000001_merged_r1.fastq.gz
+ outputs/individuals/000001/merged_fastqs/000001_merged_r2.fastq.gz
+ outputs/individuals/000002/merged_fastqs/000002_merged_r1.fastq.gz
+ outputs/individuals/000002/merged_fastqs/000002_merged_r2.fastq.gz
+ outputs/individuals/000003/merged_fastqs/000003_merged_r1.fastq.gz
+ outputs/individuals/000003/merged_fastqs/000003_merged_r2.fastq.gz
+ outputs/families/000001/000001.csv
+"
+do
+ ls $f > /dev/null
+ test_exit_status=$(( $test_exit_status + $? ))
+done
+
+echo "Test case 2: MD5 errors"
+run_nextflow ../pipeline/main.nf --ped_file assets/input_data/ped_files/batch_2_md5_errors.ped --sample_sheet assets/input_data/sample_sheets/batch_2_md5_errors.tsv $common_args
+if [ $? == 0 ]
+then
+ test_exit_status=$(( $test_exit_status + 1 ))
+fi
+
+echo "Tests finished with exit status $test_exit_status"
diff --git a/tests/scripts/bcbio_nextgen.py b/tests/scripts/bcbio_nextgen.py
new file mode 100755
index 0000000000000000000000000000000000000000..6da7b2cd0134ac67ffee297f8a64b0fb698f0150
--- /dev/null
+++ b/tests/scripts/bcbio_nextgen.py
@@ -0,0 +1,21 @@
+#!/usr/bin/env python
+"""
+Fake BCBio for testing with the empty datasets from tests/assets/
+"""
+
+import argparse
+
+def main():
+ a = argparse.ArgumentParser()
+ a.add_argument('positionals', nargs='+')
+ a.add_argument('-w')
+ a.add_argument('-n', type=int, default=16)
+ a.add_argument('-t', default='local')
+ args = a.parse_args()
+
+ if args.w:
+ open(args.positionals[1].split('-')[0] + '.yaml', 'w').close()
+
+
+if __name__ == '__main__':
+ main()
diff --git a/tests/scripts/bcbio_prepare_samples.py b/tests/scripts/bcbio_prepare_samples.py
new file mode 100755
index 0000000000000000000000000000000000000000..2da027471010c49cb6d985efe7ab2899605ccbd1
--- /dev/null
+++ b/tests/scripts/bcbio_prepare_samples.py
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+"""
+Fake BCBio prepare script for testing with the empty datasets from tests/assets/
+"""
+
+import os
+import argparse
+
+def main():
+ a = argparse.ArgumentParser()
+ a.add_argument('--out')
+ a.add_argument('--csv')
+ args = a.parse_args()
+
+ open(args.csv, 'w').close()
+
+
+if __name__ == '__main__':
+ main()
diff --git a/tests/scripts/test_config.sh b/tests/scripts/test_config.sh
new file mode 100644
index 0000000000000000000000000000000000000000..5ddda73556a1a299df097abb5b8cdc64d96f08c9
--- /dev/null
+++ b/tests/scripts/test_config.sh
@@ -0,0 +1,18 @@
+
+function run_nextflow {
+ # Run NextFlow in the background, wait for termination and return an exit status based on
+ # error occurrence. We have to do this because NextFlow doesn't like CI environments with
+ # detached stdin/stdout.
+
+ nextflow run -bg $*
+ nextflow_pid=$(cat .nextflow.pid)
+
+ while kill -0 $nextflow_pid 2> /dev/null
+ do
+ sleep 1
+ done
+ rm .nextflow.pid
+
+ # janky, but couldn't find any other way of getting the exit status
+ return "$(grep -c ERROR .nextflow.log)"
+}
diff --git a/tests/software/bazam.jar b/tests/software/bazam.jar
new file mode 100644
index 0000000000000000000000000000000000000000..a20fc23c7ca6bd2bcb5513e628f3a84763cea942
Binary files /dev/null and b/tests/software/bazam.jar differ