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nf-core_modules/tests/modules/stringtie/merge/test.yml

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Fix more version commands (#750) * Fix outstanding tests * Fix more version commands * Fix remaining modules
2021-09-28 05:56:27 +00:00
- name: stringtie merge forward-strand
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_forward_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
Add stringtie merge module (from nanoseq modules) (#475) * add stringtie merge module * add md5sum and path for stringtie.merged.gtf * fix errors * try fixing stringtie check error * add tag * remove unreproducible md5sum * address PR suggestions * hopefully fix linting error
2021-05-03 05:18:51 +00:00
tags:
- stringtie
- stringtie/merge
files:
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/stringtie.merged.gtf
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: d959eb2fab0db48ded7275e0a2e83c05
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab
md5sum: adbedee7b2f84c70362ad6dfa57442b7
- path: output/stringtie/test.ballgown/i2t.ctab
md5sum: 658131af118cfb416939044fdb5411de
- path: output/stringtie/test.ballgown/i_data.ctab
md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
- path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf
- path: output/stringtie/test.gene.abundance.txt
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: 8bcd8e2730ed3337e2730186dbc184f3
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/test.transcripts.gtf
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: a914bd55b68a4b5f607738b17861e362
Add stringtie merge module (from nanoseq modules) (#475) * add stringtie merge module * add md5sum and path for stringtie.merged.gtf * fix errors * try fixing stringtie check error * add tag * remove unreproducible md5sum * address PR suggestions * hopefully fix linting error
2021-05-03 05:18:51 +00:00
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- name: stringtie merge test_stringtie_reverse_merge
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
Add stringtie merge module (from nanoseq modules) (#475) * add stringtie merge module * add md5sum and path for stringtie.merged.gtf * fix errors * try fixing stringtie check error * add tag * remove unreproducible md5sum * address PR suggestions * hopefully fix linting error
2021-05-03 05:18:51 +00:00
tags:
- stringtie
- stringtie/merge
files:
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/stringtie.merged.gtf
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: 6da479298d73d5b3216d4e1576a2bdf4
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/test.ballgown/e2t.ctab
md5sum: 9ae42e056c955a88a883e5e917840d77
- path: output/stringtie/test.ballgown/e_data.ctab
md5sum: fd8496d3957ade3b2c0853155f9a67da
- path: output/stringtie/test.ballgown/i2t.ctab
md5sum: 658131af118cfb416939044fdb5411de
- path: output/stringtie/test.ballgown/i_data.ctab
md5sum: f01d94a7d0dcfad3bfab18ed50dad16c
- path: output/stringtie/test.ballgown/t_data.ctab
md5sum: 92a98902784e7406ffe054d2adbabc7c
- path: output/stringtie/test.coverage.gtf
- path: output/stringtie/test.gene.abundance.txt
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
Update checksum modules using human GTF (#900) * update test yml star align * update test yml stringtie merge * update star genomegenerate yml * update test yml rsem calculateexpression Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-26 22:09:04 +00:00
- path: output/stringtie/test.transcripts.gtf
Rename process from STRINGTIE to STRINGTIE_STRINGTIE (#1546) * Rename process from STRINGTIE to STRINGTIE_STRINGTIE * Bump Stringtie version to 2.2.1 and remove empty files in tests * Fix tests for stringtie/merge Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 14:13:06 +00:00
md5sum: 9dcdc9577c0fdbb25089eda210267546
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