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nf-core_modules/tests/modules/seqkit/split2/test.yml

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try to make a single test pass on GHA, passes locally
2021-02-24 03:48:55 -05:00
- name: seqkit split2 single-end length
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/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
try to make a single test pass on GHA, passes locally
2021-02-24 03:48:55 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
try to make a single test pass on GHA, passes locally
2021-02-24 03:48:55 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
Add beautiful md5sums
2021-02-23 08:57:07 -05:00
Add all tests back in
2021-02-24 03:57:23 -05:00
- name: seqkit split2 single-end size
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/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
Add all tests back in
2021-02-24 03:57:23 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
Add all tests back in
2021-02-24 03:57:23 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
Add tests for different options
2021-02-23 05:14:51 -05:00
Add all tests back in
2021-02-24 03:57:23 -05:00
- name: seqkit split2 single-end part
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/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
Add all tests back in
2021-02-24 03:57:23 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
Add all tests back in
2021-02-24 03:57:23 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
- path: output/seqkit/test.split/test_1.part_003.fastq.gz
md5sum: 8bc86ba83a611c54f592f4eae19b680f
Add tests for different options
2021-02-23 05:14:51 -05:00
Add all tests back in
2021-02-24 03:57:23 -05:00
- name: seqkit split2 paired-end length
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/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
Add all tests back in
2021-02-24 03:57:23 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
Add all tests back in
2021-02-24 03:57:23 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: 6f7d58ba35c254c0817fe9a7c69862e4
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: cf38c51506e45380fe25abdd1bd5ccc6
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
md5sum: 6b094b1ba7c439fe44c1bb5e99a02ba4
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
md5sum: 927097c6ac7522199a9e016333181a8e
Add tests for different options
2021-02-23 05:14:51 -05:00
Add all tests back in
2021-02-24 03:57:23 -05:00
- name: seqkit split2 paired-end size
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/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
Add all tests back in
2021-02-24 03:57:23 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
Add all tests back in
2021-02-24 03:57:23 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: bf835e685d597fc1ab5e5ac7dd689619
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: 703d95ff4fbb5b7fb4da8a164ba9aa54
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
md5sum: 09d0dd83b5b1b9b95d316eeed79ea5ba
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
md5sum: 8796c3f327b1094244bfcdb36d536526
Add tests for different options
2021-02-23 05:14:51 -05:00
Add all tests back in
2021-02-24 03:57:23 -05:00
- name: seqkit split2 paired-end part
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/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
Add all tests back in
2021-02-24 03:57:23 -05:00
tags:
- seqkit
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 04:10:52 -04:00
- seqkit/split2
Add all tests back in
2021-02-24 03:57:23 -05:00
files:
Remove def from module options definition in main (#270) * Remove def from module options definition in main * Fix bismark_deduplicate tests * Fix bwameth_align tests * Fixing gatk4 conda tests ("=" instead of ':' in build id) * Same as previous commit (Fix gatk4 test) * Fix qualimap bamqc test (no md5 check for pngs) * Fix seqkit split2 tests. Changed to new test data * Fix samtools tests. Some were missing initOptions include * Removing TOOL SUBTOOL template module since now it is included on tools repo
2021-03-15 08:16:43 -04:00
- path: output/seqkit/test.split/test_1.part_001.fastq.gz
md5sum: fa25951435471238d5567fd2cae31f55
- path: output/seqkit/test.split/test_1.part_002.fastq.gz
md5sum: 1dcf631aaaa5e7e0bd6c9668fbc6e04a
- path: output/seqkit/test.split/test_1.part_003.fastq.gz
md5sum: 8bc86ba83a611c54f592f4eae19b680f
- path: output/seqkit/test.split/test_2.part_001.fastq.gz
md5sum: f0055c99cd193fd97466b3cde9dd1b8f
- path: output/seqkit/test.split/test_2.part_002.fastq.gz
md5sum: 8a90df768201785f7a7cd5dbb41e846a
- path: output/seqkit/test.split/test_2.part_003.fastq.gz
md5sum: 890b90083e8e1606bd13ba34149cedd7
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