feat: addition of test files. CI testing

.github/workflows/testing.yml

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+name: Snakemake Testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Linting
+        uses: snakemake/snakemake-github-action@v1
+        with:
+          directory: '.test'
+          snakefile: '.test/Snakefile'
+          args: '--lint'
+
+      - name: Testing
+        uses: snakemake/snakemake-github-action@v1
+        with:
+          directory: '.test'
+          snakefile: '.test/Snakefile'
+          args: '--cores 1 --use-conda --conda-cleanup-pkgs cache'
+          stagein: '' # additional preliminary commands to run (can be multiline)
+          show-disk-usage-on-error: true

.test/Snakefile

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+container: "docker://continuumio/miniconda3"
+configfile: "config/config.yaml"
+include: "rules/common.smk"
+
+
+rule targets:
+    input:
+        vcf=expand(
+         os.path.join(
+            config['output_folder'],
+            "vcfs",
+            "filtered",
+            "{patient}.filtered.vcf.gz"
+         ), patient=patients
+         ),
+        idx=expand(
+         os.path.join(
+            config['output_folder'],
+            "vcfs",
+            "filtered",
+            "{patient}.filtered.vcf.gz.tbi"
+         ), patient=patients
+         )
+include: "../workflow/rules/alignment.smk"
+include: "../workflow/rules/preprocessing.smk"
+include: "../workflow/rules/somatic.smk"

.test/config/config.yaml

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+# One between ["WES", "WGS"]
+sequencing_type: "WES"
+tumor_only: true
+viral_integrated: true
+virus_name: "MCPyV"
+
+# PATH to relevant files
+units: "units.csv"
+patients: "patients.csv"
+
+# DIRECTIVES
+output_folder: "output/"
+tmp_dir: "tmp"
+log_folder: "logs/"
+
+# RESOURCES
+resources:
+  assembly: "GRCh38"
+  genomic_regions: "ref/hg38_chr22_targets.bed"
+  viral_genome: "ref/MPCyV_genome.fa"
+  reference_fasta: "ref/GRCh38_chr22.fasta"
+  dbsnps: "ref/dbsnp_146.hg38.vcf.gz"
+  known-indels: "ref/Homo_sapiens_assembly38.known_indels.vcf.gz"
+  1000g: "ref/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
+  gnomad: "ref/af-only-gnomad.hg38.vcf.gz"
+  contamination: "ref/small_exac_common_3.hg38.vcf.gz"
+  PoN: "ref/1000g_pon_hg38.vcf.gz"
+  vep_cache: ""
+
+
+# CONTAINERS
+containers:
+  ctgflow_core: "docker://danilotat/ctgflow_core"
+  qc: ""
+  deepvariant: "docker://google/deepvariant:1.8.0"
+  deepsomatic: "docker://google/deepsomatic:1.8.0"
+
+# PARAMS
+params:
+  mutect2:
+    num_workers: 10
+    args: --max-population-af 0.05 --genotype-germline-sites --linked-de-bruijn-graph --dont-use-soft-clipped-bases
+    filtering: --max-events-in-region 4 --unique-alt-read-count 2 --min-reads-per-strand 1 --min-allele-fraction 0.001
+  vep:
+    assembly: "GRCh38"
+    threads: 4
+    extra: "--pick --af --check_existing --coding_only --format vcf --vcf --symbol --terms SO --no_intergenic --tsl"
+
+

.test/patients.csv

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+patient
+pat01

.test/ref/GRCh38_chr22.dict

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+@HD	VN:1.6
+@SQ	SN:chr22	LN:50818468	M5:bd85195c4feed92050f02aabe5664435	UR:file:/Volumes/HD2/home/danilo/ctgflow/.test/ref/GRCh38_chr22.fasta

.test/ref/GRCh38_chr22.fasta.fai

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+chr22	50818468	7	70	71

.test/ref/MPCyV_genome.dict

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+@HD	VN:1.6
+@SQ	SN:NC_010277.2	LN:5387	M5:203e8a9fe025df02a3869bf2c473977e	UR:file:/Volumes/HD2/home/danilo/ctgflow/.test/ref/MPCyV_genome.fa

.test/ref/MPCyV_genome.fa

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+>NC_010277.2 Merkel cell polyomavirus isolate R17b, complete genome
+CTTGTCTATATGCAGAAGGAGTTTGCAGAAAGAGCAGAGGAGCAAATGAGCTACCTCACTAAGGAGTGGT
+TTTTATACTGCAGTTTCCCGCCCTTGGGATCTGCCCTTAGATACTGCCTTTTTTGCTAATTAAGCCTCTT
+AAGCCTCAGAGGCCTCTCTCTTTTTTTTCCAGAGGCCTCGGAGGCTAGGAGCCCCAAGCCTCTGCCAACT
+TGAAAAAAAAAAGTCACCTAGGCAGCCAAGTTGTGGTTACATGATTGAACTTTTATTGCTGCAGGGTTTC
+TGGCATTGACTCATTTCCTGGAGAGGCGGAGTTTGACTGATAAACAAAACTTTTTTTCTTTCTGTTTGGG
+AGGGAGACGGAAGACTCTTAACTTTTTTTCAACAAGGGAGGCCCGGAGGCTTTTTTTTCTCTTACAAAGG
+GAGGAGGACATTAAAAGAGTAAGTATCCTTATTTATTTTTCAGGATGGGGGGCATCATCACACTGCTGGC
+CAATATTGGTGAAATTGCTACTGAACTAAGTGCCACCACAGGAGTAACTTTGGAAGCTATTCTTACAGGA
+GAAGCTTTAGCAGCTTTGGAAGCAGAGATCTCCAGTTTAATGACAATTGAGGGTATTTCTGGCATTGAGG
+CTTTAGCTCAACTTGGGTTCACAGCTGAACAGTTTTCAAATTTCTCATTAGTGGCTTCTTTGGTTAACCA
+AGGTTTAACTTATGGCTTCATTCTCCAAACTGTTAGTGGTATAGGCTCTCTAATAACTGTGGGGGTGAGG
+TTGTCACGCGAGCAAGTGTCACTTGTAAAGAGGGATGTTTCGTGGGTAGGTAGTAATGAGGTTTTGAGGC
+ATGCACTTATGGCCTTTAGCCTAGATCCTCTGCAGTGGGAAAATAGCTTGCTGCATTCTGTGGGGCAAGA
+TATTTTTAATTCTTTATCTCCTACCTCTAGGCTGCAGATACAATCAAACCTAGTGAATCTGATACTAAAT
+AGCCGGTGGGTCTTTCAGACAACTGCTTCTCAGAATCAGGGCCTTTTATCAGGAGAGGCTATATTAATTC
+CTGAACATATAGGAGGAACTCTGCAGCAGCAAACTCCAGATTGGCTTCTTCCTCTGGTACTAGGCCTTAG
+TGGATATATTTCTCCTGAATTACAAGTAATTGAAGATGGCACCAAAAAGAAAAGCATCATCCACCTGTAA
+AACACCCAAAAGACAATGTATACCTAAGCCGGGATGCTGCCCTAATGTTGCCTCAGTTCCAAAACTGCTT
+GTTAAAGGAGGAGTGGAAGTATTATCTGTGGTTACTGGAGAAGATAGCATTACCCAAATTGAGTTGTATT
+TGAATCCAAGAATGGGAGTTAATTCCCCTGATCTTCCTACTACTTCAAACTGGTATACTTATACTTATGA
+CCTGCAGCCAAAGGGATCATCTCCAGATCAGCCCATCAAGGAAAATTTGCCAGCTTACAGTGTGGCAAGA
+GTGTCTCTGCCAATGCTAAATGAGGATATTACCTGTGACACATTGCAGATGTGGGAGGCAATATCTGTTA
+AAACAGAAGTAGTTGGAATAAGTTCTTTAATTAATGTTCATTATTGGGACATGAAAAGAGTTCATGATTA
+TGGTGCTGGTATTCCTGTGTCAGGGGTAAATTACCATATGTTTGCCATTGGGGGAGAACCTCTGGATTTG
+CAAGGCCTAGTTTTAGATTACCAGACTGAGTATCCAAAAACTACAAATGGTGGGCCTATTACAATTGAAA
+CTGTATTGGGAAGAAAAATGACACCTAAAAATCAGGGCCTAGATCCACAAGCTAAAGCAAAATTAGATAA
+AGATGGAAATTATCCTATAGAAGTATGGTGTCCTGATCCTTCTAAAAATGAAAACAGTAGATACTATGGG
+TCTATTCAGACAGGCTCTCAGACTCCTACAGTTCTTCAATTTAGTAATACTCTAACTACTGTCCTTTTAG
+ATGAGAATGGAGTGGGCCCTCTATGCAAAGGAGATGGCCTATTTATTAGCTGTGCAGACATAGTGGGGTT
+TCTGTTTAAAACCAGTGGAAAAATGGCTCTTCATGGGTTGCCTAGATATTTTAATGTTACTTTGAGAAAA
+AGATGGGTGAAAAACCCCTACCCAGTAGTTAATTTAATAAACTCACTCTTCAGCAACTTAATGCCAAAAG
+TGTCAGGCCAACCTATGGAAGGAAAAGATAATCAGGTAGAAGAGGTTAGAATATATGAGGGGTCAGAACA
+ATTACCTGGTGATCCTGATATTGTCAGATTTTTAGATAAATTTGGGCAGGAGAAAACTGTTTACCCAAAG
+CCCTCTGTTGCCCCAGCAGCAGTAACATTCCAAAGTAATCAGCAGGATAAGGGCAAGGCGCCACTGAAAG
+GACCTCAAAAGGCCTCTCAAAAAGAAAGCCAAACACAAGAATTATGAGAATTATTTCATGCATTCCTATT
+CAGTTAAGTAGGCCCCAGAAAAACAAACACAGGAAATATGAAGCAGATGCCTTTATTGAGAAAAAGTACC
+AGAATCTTGGGTTTCTTCAGTTTCCTCAGGGCCCTCTTCCTCAATAAGAATATTGAGCAGAGGGTCCTGA
+CCAGCTTCTACATTTTCTATCATTTGACAAAATTTACCATATGATATTTCACTCTGTAAAATTTGCTTCC
+AGTTTTTAATTTCTTCTTGTAAGCAAGGCTTAAAGGTTGTATCAGGCAAGCACCAAATAAGACAAAGCAA
+TAAAGTGGTTCCACTTTGAAGAATTCTTCTTTTTCTTATTTCCATGTTCTGATCCAGGGAATCTCTTAGA
+TTTGCCTTTGGGGAAAAGTGTAAAGTATAACTAAATCTTGCTATTAATGTTTTGGGAATAAAATAATCAT
+TAGCAGTAACAATACAAGGAGGAAAAATCTGATGCTTTTTATTCACATGCTTCTTCTCTAAGCTTACAGC
+TACAGCACCATCTAGATGATCTCTTAAGTTATCAAGGTTATTTATTCCTTGCCCTGGTTGCAGATCTTTA
+TTTAGGCTATTTTGCCCTTTCACATCCTCAAAAACAACCATAAATTTATCCAAAGCACATCCTAGTTCAA
+AAGGCAGTTTATCAGATGGACAGTTTATATTCAAGGCCTTCCCTTCTAGCAAATCTATTAAGGCTGCAGC
+AAAGCTTGTTTTTCCACTGTTAATAGGCCCTTTAAACCAAATGTTTCTATACTTAGGTATATTCTCTGTT
+AATAATTGAATAATTTTCTGCAGCTTCTTTTCAAACTCTTCAAATAAGCAGCAGTACCAGGCCACACCAC
+CCATATAATACAGTAGATCTATTGTATCTAAATCTCTTAATCTCTCTAGGTGCTTCTTAAACTTCTTACA
+TAGCATTTCTGTCCTGGTCATTTCCAGCATCTCTAACCTCCTTTTGGCTAGAACAGTGTCTGCGGCTTGT
+TGGCAAATGGTTTTCTGAGATTTAGATTCATAAAATAGCTTAGCATTAGAATGATGAGCCTCATGAGCCT
+TGTGAGGTTTGAGGCGAGATCTGTTTTCACACTTTTGGCAAGGAAATGGTTTTGCAAAGTCTAGATAATG
+GGCTAAGATAATAAAGTGGTCGTCTAGCTCATATTCACAAGCAAATTCAGCAACTAAATTCCAATTACAG
+CTGGCCTCTTTTTCTTTTTCTTGAAATTCATAATTGAGCAGTGGCTTATTCTCTTGCAGTAATTTGTAAG
+GGGGCTTGCATAAATTATTATACATTTCAGGCATCTTATTCACTCCTTTACAAATTAAAAAGCTTATAGT
+GCAGAAGGTAGAGCAAAAATTCTTAATAGCAGATACTCTATGCTTTGATAAAGTTATAAACAATAAAATA
+CATCCTAATTCACAGGCATGCCTGCTTTTAAAATCAACTTTAAATTTCTCAATCTTATCATATAACTCTA
+TAGCTTTATCAGAAGTAGTATAAATGGCAAAACAACTTACTGTTTTATTACTATATACAGCATGGCTAAG
+ATAATCAGAAAGATCAATAGGAAAATCAGTAGGAACAGGAGTTTCTCTGTTCTTTTTTGGCTTTGGTGGA
+GTGCTTGTAAAACTTGCTGAACTAGCAGAGCTTGCAGAGCTTCGGGACCCCCCAAATTTTCGCTTTCTTG
+AGAATGGAGGAGGGGTCTTCGGGGTGGTGAAGGAGGAGGATCTGTATTCCTCATCTGTAAACTGAGATGA
+CGAGGCCTCCTCGGCAGAGGAAGACGGGGGCTGCCGGGGCGAGCTTCTTGAGGAGGGGGGCTCCTCAGGC
+TCCTCAGAGGACGAGGGAGGCTCAGGGGAGGAAAGTGATTCATCGCAGAAGAGATCCTCCCAGGTGCCAT
+CCGTTCTGGAAGAATTTCTAGGTACACTGGTTCCATTGGGTGTGCTGGATTCTCTTCCTGAATTGGTGGT
+CTCCTCTCTGCTACTGGATCCAGAGGATGAGGTGGGTTCCTCATGGTGTTCGGGAGGTATATCGGGTCCT
+CTGGACTGGGAGTCTGAAGCCTGGGACGCTGAGAAGGACCCATACCCAGAGGAAGAGCTCTGGCTGTGGG
+GTGGTGAGCTTCCACTGGGGGCTCCCCTGGATGCATTGGAGGAAGGCTTTCTGGATCTTGAGTTGGTCCC
+GTGTGGATTGGGCCCATATTCGTATGCCTTCCCGAAGCTGAATCCTCCTGATCTCCACCATTCTTTGAAT
+TTAGTGGTCCCATATATAGGGGCCTCGTCAACCTAGATGGGAAAGTACAGAAAATCTGTCATAAATAACC
+TTTCTTTGATATTTTGCCTTATAGACTTTTCCATATCTAATACTTACAGAGGAAGGAAGTAGGAGTCTAG
+AAAAGGTGCAGATGCAGTAAGCAGTAGTCAGTTTCTTCTAAAGTTTTTTGCCACCAGTCAAAACTTTCCC
+AAGTAGGAGGAAATCCAAACCAAAGAATAAAGCACTGATAGCAAAAACACTCTCCCCACGTCAGACAGTT
+TTTTTGCTTTAAAGTTTTTAGACTACAATGCTGGCGAGACAACTTACAGCTAATACAAGCGCACTTAGAA
+TCTCTAAGTTGCTTAAGCATGCACCCAGGACCTCTGCAAAATCTAGCATTATATCCACTTTGCATATAAT
+CCTTTAAAGTTCCATATTCTTCCCAAGGAAATTTTGTACTGACCTCATCAAACATAGAGAAGTCACTTCT
+GAGCTTGTGGATATTTTGCTGGAATTTGCTCCAAAGGGTGTTCAATTCCATCATTATAACAGGATTTCCC
+CCTTTATCAGGGTGATGCTTTAAGCAGCTTCTTTTGAAAGCAGCTTTCATCAGAGGGATGTTGCCATAAC
+AATTAGGAGCAATCTCTAAAAGCTTGCAGAGAGCCTCTCTTTCTTTCCTATTTAGGACTAAATCCAT