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a740a6ff48
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
35 lines
1 KiB
YAML
35 lines
1 KiB
YAML
- name: checkm lineagewf
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command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c tests/config/nextflow.config
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tags:
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- checkm
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- checkm/lineagewf
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files:
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- path: output/checkm/test.tsv
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md5sum: d5559764f563c4b55223e4e4a3dc1ec9
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- path: output/checkm/test/checkm.log
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contains:
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- "INFO: Parsing HMM hits to marker genes:"
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- path: output/checkm/test/lineage.ms
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contains:
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- "# [Lineage Marker File]"
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- "contigs"
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- "UID1"
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- name: checkm lineagewf_multi
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command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c tests/config/nextflow.config
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tags:
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- checkm
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- checkm/lineagewf
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files:
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- path: output/checkm/test.tsv
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md5sum: 7e0fa177dcf151b84b7751813fbde3d1
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- path: output/checkm/test/checkm.log
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contains:
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- "INFO: Parsing HMM hits to marker genes:"
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- path: output/checkm/test/lineage.ms
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contains:
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- "# [Lineage Marker File]"
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- "contigs"
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- "UID1"
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- "genome"
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