- name: gtdb-test
  command: bash -c 'nextflow run ./subworkflows/local/gtdb/test.nf -entry test_gtdb --wf gtdb --max_memory 64 -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - gtdb
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/gtdb/merged-results/gtdb.tsv
      md5sum: b5c28efee7a7a397284a82282d38724d
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-dag.dot
      contains: ['gtdbdag', 'GTDB', 'versions']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-trace.txt
      contains: ['task_id']
    - path: bactopia/test/tools/gtdb/align/test.bac120.filtered.tsv
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/align/test.bac120.msa.fasta.gz
    - path: bactopia/test/tools/gtdb/align/test.bac120.user_msa.fasta.gz
    - path: bactopia/test/tools/gtdb/classify/test.bac120.classify.tree.1.tree
      md5sum: 4050dedc41112a616ee3e045b359a8b1
    - path: bactopia/test/tools/gtdb/classify/test.bac120.classify.tree.6.tree
      md5sum: 9f1a7efa6725335378b1039b085c0ab7
    - path: bactopia/test/tools/gtdb/classify/test.bac120.summary.tsv
    - path: bactopia/test/tools/gtdb/classify/test.bac120.tree.mapping.tsv
      md5sum: 61e7eec11349926af6613684b64d4321
    - path: bactopia/test/tools/gtdb/classify/test.backbone.bac120.classify.tree
      md5sum: 5232b60db0bcf21c22c07cdb19baf690
    - path: bactopia/test/tools/gtdb/gtdbtk.json
    - path: bactopia/test/tools/gtdb/identify/test.ar53.markers_summary.tsv
      md5sum: 18b16607512b160bade65758082fb704
    - path: bactopia/test/tools/gtdb/identify/test.bac120.markers_summary.tsv
      md5sum: 4395dba453d660d5b0772ffd8f338946
    - path: bactopia/test/tools/gtdb/identify/test.failed_genomes.tsv
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/identify/test.translation_table_summary.tsv
      md5sum: d7b6fa452dc8efd2cb604dd4ad438fe7
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.err
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.log
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.out
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.sh
      contains: ['gtdb', 'END_VERSIONS']
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.trace
      contains: ['nextflow.trace']
    - path: bactopia/test/tools/gtdb/logs/results/gtdbtk.log
    - path: bactopia/test/tools/gtdb/logs/results/gtdbtk.warnings.log
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/logs/versions.yml
      md5sum: 8f1ba835539a56837d6e85debdbe8721
    - path: bactopia/test/tools/gtdb/test.bac120.summary.tsv

- name: gtdb-test-tarball
  command: bash -c 'nextflow run ./subworkflows/local/gtdb/test.nf -entry test_gtdb_tarball --wf gtdb --max_memory 64 -c nextflow.config ${BACTOPIA_ARGS}'
  tags:
    - gtdb
    - gtdb-tarball
    - bactopia-tools
  files:
    - path: bactopia/bactopia-runs/gtdb/merged-results/gtdb.tsv
      md5sum: b5c28efee7a7a397284a82282d38724d
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.err
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.log
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.out
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.sh
      contains: ['csvtk', 'END_VERSIONS']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/nf-merged-results.trace
      contains: ['nextflow.trace']
    - path: bactopia/bactopia-runs/gtdb/merged-results/logs/gtdb-concat/versions.yml
      contains: ['csvtk']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-dag.dot
      contains: ['gtdbdag', 'GTDB', 'versions']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-report.html
      contains: ['html', 'Nextflow', 'Report']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-timeline.html
      contains: ['html', 'Nextflow', 'timeline']
    - path: bactopia/bactopia-runs/gtdb/nf-reports/gtdb-trace.txt
      contains: ['task_id']
    - path: bactopia/test/tools/gtdb/align/test.bac120.filtered.tsv
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/align/test.bac120.msa.fasta.gz
    - path: bactopia/test/tools/gtdb/align/test.bac120.user_msa.fasta.gz
    - path: bactopia/test/tools/gtdb/classify/test.bac120.classify.tree.1.tree
      md5sum: 4050dedc41112a616ee3e045b359a8b1
    - path: bactopia/test/tools/gtdb/classify/test.bac120.classify.tree.6.tree
      md5sum: 9f1a7efa6725335378b1039b085c0ab7
    - path: bactopia/test/tools/gtdb/classify/test.bac120.summary.tsv
    - path: bactopia/test/tools/gtdb/classify/test.bac120.tree.mapping.tsv
      md5sum: 61e7eec11349926af6613684b64d4321
    - path: bactopia/test/tools/gtdb/classify/test.backbone.bac120.classify.tree
      md5sum: 5232b60db0bcf21c22c07cdb19baf690
    - path: bactopia/test/tools/gtdb/gtdbtk.json
    - path: bactopia/test/tools/gtdb/identify/test.ar53.markers_summary.tsv
      md5sum: 18b16607512b160bade65758082fb704
    - path: bactopia/test/tools/gtdb/identify/test.bac120.markers_summary.tsv
      md5sum: 4395dba453d660d5b0772ffd8f338946
    - path: bactopia/test/tools/gtdb/identify/test.failed_genomes.tsv
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/identify/test.translation_table_summary.tsv
      md5sum: d7b6fa452dc8efd2cb604dd4ad438fe7
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.begin
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.err
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.log
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.out
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.run
      contains: ['NEXTFLOW TASK', '$NXF_ENTRY']
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.sh
      contains: ['gtdb', 'END_VERSIONS']
    - path: bactopia/test/tools/gtdb/logs/nf-gtdb.trace
      contains: ['nextflow.trace']
    - path: bactopia/test/tools/gtdb/logs/results/gtdbtk.log
    - path: bactopia/test/tools/gtdb/logs/results/gtdbtk.warnings.log
    - path: bactopia/test/tools/gtdb/logs/versions.yml
      md5sum: e4de046f9fcfa50e94a9ccab2516ace1
    - path: bactopia/test/tools/gtdb/test.bac120.summary.tsv
