- name: snippy-test
  command: bash -c 'nextflow run ./subworkflows/local/snippy/test.nf -entry test_snippy --wf snippy -c nextflow.config --min_window_size 5000 --mincov 1 --minqual 1 --basequal 1 --mapqual 1 --maxsoft 1 ${BACTOPIA_ARGS}'
  tags:
    - snippy
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/snippy/core-snp-clean.full.aln.gz
    - path: bactopia/bactopia-runs/snippy/core-snp.full.aln.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.branch_base_reconstruction.embl.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.filtered_polymorphic_sites.fasta.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.filtered_polymorphic_sites.phylip
      md5sum: d7318d1e1e3497bc6c268dae34972f1e
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.final_tree.tre
      md5sum: 78c79b29a36a34548fdc59aed29343b4
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.node_labelled.final_tree.tre
      md5sum: 95a00666f6e7f04b5dcf8fa3b9ec30b5
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.per_branch_statistics.csv
      md5sum: b9deecaf94fb3049956356c1ecc7c10e
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.recombination_predictions.embl.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.recombination_predictions.gff.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.summary_of_snp_distribution.vcf.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/core-snp.log
      contains: ["Process", "raxml", "Model", "Gubbins"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.err
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.log
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.out
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.sh
      contains: ['gubbins', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/versions.yml
      md5sum: 06e837b60e52d63b0f5b53d25f63924d
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.alninfo
      md5sum: b0fba4469a915df9872ca077eb2cf808
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.bionj
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.ckp.gz
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.contree
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.iqtree
      contains: ['REFERENCES', 'test1', 'Total']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.mldist
      contains: ['Reference', 'test0', 'test4']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.splits.nex
      contains: ['TAXLABELS', 'test2', 'END']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.treefile
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.ufboot
      contains: ['test1', 'test2', 'test3']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/core-snp.log
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.err
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.log
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.out
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.sh
      contains: ['iqtree', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/versions.yml
      md5sum: c04a175666aaa68582bb36208ee37733
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-dag.dot
      contains: ['snippydag', 'SNIPPY', 'versions']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-trace.txt
      contains: ['task_id']
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.aln.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.tab.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.txt
      md5sum: e08c4a322958008c3ead372cbf9d05c4
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.vcf.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.err
      contains: ['test', 'core-snp', 'Done', 'snippy-core']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.log
      contains: ['test', 'core-snp', 'Done', 'snippy-core']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.sh
      contains: ['snippy-core', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/versions.yml
      md5sum: 0362757dde048c5c4f118e8ec2256330
    - path: bactopia/bactopia-runs/snippy/snpdists/core-snp.distance.tsv
      md5sum: eca1078f443287c1bfdac84cdbce50b5
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.err
      contains: ['snp-dists', 'Read']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.log
      contains: ['snp-dists', 'Read']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.out
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.sh
      contains: ['snp-dists', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/versions.yml
      md5sum: 15c50a79a2e8f5a96107199f849a9a77
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.err
      contains: ["snippy", "Running", "test0", "Done"]
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.log
      contains: ["snippy", "Running", "test0", "Done"]
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.out
      md5sum: fa319889ecf3bef06c44f7c1e989f018
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.sh
      contains: ['snippy', 'END_VERSIONS']
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.trace
      contains: ['nextflow.trace']
    - path: bactopia/test0/tools/snippy/snippy/logs/test0.log
      contains: ["snippy", "snpEff", "test0", "consensus"]
    - path: bactopia/test0/tools/snippy/snippy/logs/versions.yml
      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
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    - path: bactopia/test0/tools/snippy/snippy/test0.annotated.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.bam
    - path: bactopia/test0/tools/snippy/snippy/test0.bam.bai
    - path: bactopia/test0/tools/snippy/snippy/test0.bed.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.subs.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.subs.masked.fa.gz
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    - path: bactopia/test0/tools/snippy/snippy/test0.csv.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.filt.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.gff.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.html
    - path: bactopia/test0/tools/snippy/snippy/test0.raw.vcf.gz
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    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
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      contains: ["snippy", "Running", "test1", "Done"]
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      md5sum: fa319889ecf3bef06c44f7c1e989f018
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      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.sh
      contains: ['snippy', 'END_VERSIONS']
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.trace
      contains: ['nextflow.trace']
    - path: bactopia/test1/tools/snippy/snippy/logs/test1.log
      contains: ["snippy", "snpEff", "test1", "consensus"]
    - path: bactopia/test1/tools/snippy/snippy/logs/versions.yml
      md5sum: b2fc8299d29a9b4c2cda418ecb04592d
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    - path: bactopia/test1/tools/snippy/snippy/test1.annotated.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.bam
    - path: bactopia/test1/tools/snippy/snippy/test1.bam.bai
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    - path: bactopia/test1/tools/snippy/snippy/test1.consensus.fa.gz
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    - path: bactopia/test1/tools/snippy/snippy/test1.consensus.subs.masked.fa.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.coverage.txt.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.csv.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.filt.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.gff.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.html
    - path: bactopia/test1/tools/snippy/snippy/test1.raw.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.subs.vcf.gz
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      contains: ["DateTime", "ReadFiles", "VariantTotal"]
    - path: bactopia/test4/tools/snippy/snippy/test4.vcf.gz

- name: snippy-test-mask
  command: bash -c 'nextflow run ./subworkflows/local/snippy/test.nf -entry test_snippy_mask --wf snippy -c nextflow.config --min_window_size 5000 --mincov 1 --minqual 1 --basequal 1 --mapqual 1 --maxsoft 1 ${BACTOPIA_ARGS}'
  tags:
    - snippy
    - snippy-mask
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/snippy/core-snp-clean.full.aln.gz
    - path: bactopia/bactopia-runs/snippy/core-snp.full.aln.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.branch_base_reconstruction.embl.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.filtered_polymorphic_sites.fasta.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.filtered_polymorphic_sites.phylip
      md5sum: d7318d1e1e3497bc6c268dae34972f1e
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.final_tree.tre
      md5sum: 78c79b29a36a34548fdc59aed29343b4
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.node_labelled.final_tree.tre
      md5sum: 95a00666f6e7f04b5dcf8fa3b9ec30b5
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.per_branch_statistics.csv
      md5sum: b9deecaf94fb3049956356c1ecc7c10e
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.recombination_predictions.embl.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.recombination_predictions.gff.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/core-snp.summary_of_snp_distribution.vcf.gz
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/core-snp.log
      contains: ["Process", "raxml", "Model", "Gubbins"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.err
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.log
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.out
      contains: ["RAxML", "Alignment", "Substitution", "final"]
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.sh
      contains: ['gubbins', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/nf-gubbins.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/gubbins/logs/versions.yml
      md5sum: e763a9a67609a03acd4dfec3e2071234
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.alninfo
      md5sum: 3538bdd4729b861eb66eb3e69060812d
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.bionj
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.ckp.gz
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.contree
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.iqtree
      contains: ['REFERENCES', 'test1', 'Total']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.mldist
      contains: ['Reference', 'test0', 'test4']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.splits.nex
      contains: ['TAXLABELS', 'test2', 'END']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.treefile
      contains: ['test']
    - path: bactopia/bactopia-runs/snippy/iqtree/core-snp.ufboot
      contains: ['test1', 'test2', 'test3']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/core-snp.log
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.err
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.log
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.out
      contains: ['IQ-TREE', 'Ultrafast', 'Date']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.sh
      contains: ['iqtree', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/nf-iqtree.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/iqtree/logs/versions.yml
      md5sum: 553a232ace7e6bcb246b87f0e2d26752
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-dag.dot
      contains: ['snippydag', 'SNIPPY', 'versions']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/snippy/nf-reports/snippy-trace.txt
      contains: ['task_id']
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.aln.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.tab.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.txt
      md5sum: 12cbcd8946fbad8adb3f149fc876b05f
    - path: bactopia/bactopia-runs/snippy/snippy-core/core-snp.vcf.gz
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.err
      contains: ['test', 'core-snp', 'Done', 'snippy-core']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.log
      contains: ['test', 'core-snp', 'Done', 'snippy-core']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.out
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.sh
      contains: ['snippy-core', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/nf-snippy-core.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/snippy-core/logs/versions.yml
      md5sum: 02f01df9b4b6a6be837acbc9bced050a
    - path: bactopia/bactopia-runs/snippy/snpdists/core-snp.distance.tsv
      md5sum: eca1078f443287c1bfdac84cdbce50b5
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.err
      contains: ['snp-dists', 'Read']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.log
      contains: ['snp-dists', 'Read']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.out
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.sh
      contains: ['snp-dists', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/nf-snpdists.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/snippy/snpdists/logs/versions.yml
      md5sum: 3c83a09255b761100bf1866213e21ada
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.err
      contains: ["snippy", "Running", "test0", "Done"]
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.log
      contains: ["snippy", "Running", "test0", "Done"]
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.out
      md5sum: fa319889ecf3bef06c44f7c1e989f018
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.sh
      contains: ['snippy', 'END_VERSIONS']
    - path: bactopia/test0/tools/snippy/snippy/logs/nf-snippy.trace
      contains: ['nextflow.trace']
    - path: bactopia/test0/tools/snippy/snippy/logs/test0.log
      contains: ["snippy", "snpEff", "test0", "consensus"]
    - path: bactopia/test0/tools/snippy/snippy/logs/versions.yml
      md5sum: 90cc2953b8258a258cbdf45e82689115
    - path: bactopia/test0/tools/snippy/snippy/test0.aligned.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.annotated.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.bam
    - path: bactopia/test0/tools/snippy/snippy/test0.bam.bai
    - path: bactopia/test0/tools/snippy/snippy/test0.bed.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.subs.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.consensus.subs.masked.fa.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.coverage.txt.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.csv.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.filt.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.gff.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.html
    - path: bactopia/test0/tools/snippy/snippy/test0.raw.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.subs.vcf.gz
    - path: bactopia/test0/tools/snippy/snippy/test0.tab
      md5sum: fec0f789f9f36e0b125fffd2be3635be
    - path: bactopia/test0/tools/snippy/snippy/test0.txt
      contains: ["DateTime", "ReadFiles", "VariantTotal"]
    - path: bactopia/test0/tools/snippy/snippy/test0.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.err
      contains: ["snippy", "Running", "test1", "Done"]
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.log
      contains: ["snippy", "Running", "test1", "Done"]
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.out
      md5sum: fa319889ecf3bef06c44f7c1e989f018
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.sh
      contains: ['snippy', 'END_VERSIONS']
    - path: bactopia/test1/tools/snippy/snippy/logs/nf-snippy.trace
      contains: ['nextflow.trace']
    - path: bactopia/test1/tools/snippy/snippy/logs/test1.log
      contains: ["snippy", "snpEff", "test1", "consensus"]
    - path: bactopia/test1/tools/snippy/snippy/logs/versions.yml
      md5sum: 90cc2953b8258a258cbdf45e82689115
    - path: bactopia/test1/tools/snippy/snippy/test1.aligned.fa.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.annotated.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.bam
    - path: bactopia/test1/tools/snippy/snippy/test1.bam.bai
    - path: bactopia/test1/tools/snippy/snippy/test1.bed.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.consensus.fa.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.consensus.subs.fa.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.consensus.subs.masked.fa.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.coverage.txt.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.csv.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.filt.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.gff.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.html
    - path: bactopia/test1/tools/snippy/snippy/test1.raw.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.subs.vcf.gz
    - path: bactopia/test1/tools/snippy/snippy/test1.tab
      md5sum: fec0f789f9f36e0b125fffd2be3635be
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    - path: bactopia/test1/tools/snippy/snippy/test1.vcf.gz
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.err
      contains: ["snippy", "Running", "test2", "Done"]
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.log
      contains: ["snippy", "Running", "test2", "Done"]
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.out
      md5sum: fa319889ecf3bef06c44f7c1e989f018
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.sh
      contains: ['snippy', 'END_VERSIONS']
    - path: bactopia/test2/tools/snippy/snippy/logs/nf-snippy.trace
      contains: ['nextflow.trace']
    - path: bactopia/test2/tools/snippy/snippy/logs/test2.log
      contains: ["snippy", "snpEff", "test2", "consensus"]
    - path: bactopia/test2/tools/snippy/snippy/logs/versions.yml
      md5sum: 90cc2953b8258a258cbdf45e82689115
    - path: bactopia/test2/tools/snippy/snippy/test2.aligned.fa.gz
    - path: bactopia/test2/tools/snippy/snippy/test2.annotated.vcf.gz
    - path: bactopia/test2/tools/snippy/snippy/test2.bam
    - path: bactopia/test2/tools/snippy/snippy/test2.bam.bai
    - path: bactopia/test2/tools/snippy/snippy/test2.bed.gz
    - path: bactopia/test2/tools/snippy/snippy/test2.consensus.fa.gz
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    - path: bactopia/test2/tools/snippy/snippy/test2.html
    - path: bactopia/test2/tools/snippy/snippy/test2.raw.vcf.gz
    - path: bactopia/test2/tools/snippy/snippy/test2.subs.vcf.gz
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      md5sum: fec0f789f9f36e0b125fffd2be3635be
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    - path: bactopia/test2/tools/snippy/snippy/test2.vcf.gz
    - path: bactopia/test3/tools/snippy/snippy/logs/nf-snippy.begin
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      contains: ["snippy", "Running", "test3", "Done"]
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      contains: ['snippy', 'END_VERSIONS']
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      contains: ['nextflow.trace']
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      contains: ["snippy", "snpEff", "test3", "consensus"]
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      md5sum: 90cc2953b8258a258cbdf45e82689115
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    - path: bactopia/test4/tools/snippy/snippy/test4.bam.bai
    - path: bactopia/test4/tools/snippy/snippy/test4.bed.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.consensus.fa.gz
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    - path: bactopia/test4/tools/snippy/snippy/test4.coverage.txt.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.csv.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.filt.vcf.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.gff.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.html
    - path: bactopia/test4/tools/snippy/snippy/test4.raw.vcf.gz
    - path: bactopia/test4/tools/snippy/snippy/test4.subs.vcf.gz
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    - path: bactopia/test4/tools/snippy/snippy/test4.txt
      contains: ["DateTime", "ReadFiles", "VariantTotal"]
    - path: bactopia/test4/tools/snippy/snippy/test4.vcf.gz
