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nf-core_modules/tests/modules/last/train/test.yml

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New last/train module to train alignment parameters. (#492) * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 03:37:08 -04:00
- name: last train test_last_train
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 05:10:18 -04:00
command: nextflow run tests/modules/last/train -entry test_last_train -c tests/config/nextflow.config
New last/train module to train alignment parameters. (#492) * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 03:37:08 -04:00
tags:
- last/train
- last
files:
- path: output/last/contigs.genome.par
contains:
- "score matrix"
- path: output/untar/lastdb/genome.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/untar/lastdb/genome.des
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/untar/lastdb/genome.prj
md5sum: 489715f14b0fea6273822696e72357f9
- path: output/untar/lastdb/genome.sds
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
- path: output/untar/lastdb/genome.ssp
md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
- path: output/untar/lastdb/genome.suf
md5sum: 1895efa8653e8e9bd3605cff0408ed33
- path: output/untar/lastdb/genome.tis
md5sum: b7c40f06b1309dc6f37849eeb86dfd22
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