mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-26 04:18:17 +00:00
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
|
|
command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf -c tests/config/nextflow.config
|
|
tags:
|
|
- checkm
|
|
- checkm/lineagewf
|
|
files:
|
|
- path: output/checkm/test.tsv
|
|
md5sum: d5559764f563c4b55223e4e4a3dc1ec9
|
|
- path: output/checkm/test/checkm.log
|
|
contains:
|
|
- "INFO: Parsing HMM hits to marker genes:"
|
|
- path: output/checkm/test/lineage.ms
|
|
contains:
|
|
- "# [Lineage Marker File]"
|
|
- "contigs"
|
|
- "UID1"
|
|
|
|
- name: checkm lineagewf_multi
|
|
command: nextflow run ./tests/modules/checkm/lineagewf -entry test_checkm_lineagewf_multi -c tests/config/nextflow.config
|
|
tags:
|
|
- checkm
|
|
- checkm/lineagewf
|
|
files:
|
|
- path: output/checkm/test.tsv
|
|
md5sum: 7e0fa177dcf151b84b7751813fbde3d1
|
|
- path: output/checkm/test/checkm.log
|
|
contains:
|
|
- "INFO: Parsing HMM hits to marker genes:"
|
|
- path: output/checkm/test/lineage.ms
|
|
contains:
|
|
- "# [Lineage Marker File]"
|
|
- "contigs"
|
|
- "UID1"
|
|
- "genome"
|
|
|