millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-09-22 16:12:04 +00:00
Code Issues Releases Packages Activity
nf-core_modules/tests/modules/last/lastdb/test.yml

42 lines
1.6 KiB
YAML
Raw Normal View History

New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
- name: last lastdb test_last_lastdb
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
command: nextflow run tests/modules/last/lastdb -entry test_last_lastdb -c tests/config/nextflow.config
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
tags:
- last/lastdb
Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards.
2021-06-14 11:27:27 +00:00
- last
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
files:
- path: output/last/lastdb/test.bck
md5sum: 5519879b9b6c4d1fc508da7f17f88f2e
- path: output/last/lastdb/test.des
md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc
- path: output/last/lastdb/test.prj
Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards.
2021-06-14 11:27:27 +00:00
md5sum: 2c981eb9b9d2012d8413946a5b378f20
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
- path: output/last/lastdb/test.sds
md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2
- path: output/last/lastdb/test.ssp
md5sum: 4137fb6fe9df2b3d78d5b960390aac7b
- path: output/last/lastdb/test.suf
md5sum: 1895efa8653e8e9bd3605cff0408ed33
- path: output/last/lastdb/test.tis
md5sum: b7c40f06b1309dc6f37849eeb86dfd22
- name: last lastdb test_last_lastdb_gzipped_input
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 09:10:18 +00:00
command: nextflow run tests/modules/last/lastdb -entry test_last_lastdb_gzipped_input -c tests/config/nextflow.config
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
tags:
- last/lastdb
Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards.
2021-06-14 11:27:27 +00:00
- last
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
files:
- path: output/last/lastdb/test.bck
md5sum: 8692b1229b1fff1c2d39c4c610ff842b
- path: output/last/lastdb/test.des
md5sum: 26ab49015cc572172b9efa50fc5190bc
- path: output/last/lastdb/test.prj
Update last module (#533) * Update LAST to version 1238. * Update functions.nf to the latest devel version. * Update test MD5sums after updating software version. * Make portable on MacOS * Allow input alignments to be uncompressed. While the strategy in this family of modules is to make all inputs and outputs compressed, this change might be useful to some users. As of LAST 2138, `last/split` does not allow its input to be compressed. * Search for .des file, that is guaranteed to be unique. Some LAST indexes have more than one .bck file and it makes the name detection crash. In this commit, I also standardise how the names are detected. * Use value input channel and optional output channels to handle formats. As discussed on Slack, it is preferred to use a value input channel instead of sneaking options through `params.args2` or `params.format` as we did. Likewise, optional output channels with clearly labeled format are preferred to 'catch-all' wildcards.
2021-06-14 11:27:27 +00:00
md5sum: aec51a18da1c2361aaca70dd16eb7b7b
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
- path: output/last/lastdb/test.sds
md5sum: cad9927d4bd161257e98165ad755d8e4
- path: output/last/lastdb/test.ssp
md5sum: 574c8a080247c2af9b5c46ff70936186
- path: output/last/lastdb/test.suf
md5sum: 8c406111b398631e51ca79d99b0ee897
- path: output/last/lastdb/test.tis
md5sum: d57a3a5f7e3e036807356c15bd3aad97
Reference in a new issue Copy permalink