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nf-core_modules/tests/modules/damageprofiler/test.yml

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damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- name: damageprofiler
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 02:58:40 -05:00
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/3pGtoA_freq.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 61c903b1504ed7d7182570dfc75e4498
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/5pCtoT_freq.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 15a75b60ee519b61ce04a83fe3afe855
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/DamagePlot.pdf
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/dmgprof.json
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/DNA_comp_genome.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: fea48af1ecf491b439d36d4a919473df
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/DNA_composition_sample.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/editDistance.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/Length_plot_combined_data.svg
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/lgdistribution.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: df2e19195185ea9ee05e8e84b2948f36
damageprofiler (#545) * Add damageprofiler module * Fix tests * Bump container hopefully with font fix * Following code review
2021-06-30 03:46:24 -04:00
- path: output/damageprofiler/test/misincorporation.txt
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
- name: damageprofiler_reference
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 02:58:40 -05:00
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
- path: output/damageprofiler/test/3pGtoA_freq.txt
md5sum: 61c903b1504ed7d7182570dfc75e4498
- path: output/damageprofiler/test/5pCtoT_freq.txt
md5sum: 15a75b60ee519b61ce04a83fe3afe855
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/DamagePlot.pdf
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/dmgprof.json
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
- path: output/damageprofiler/test/DNA_comp_genome.txt
md5sum: fea48af1ecf491b439d36d4a919473df
- path: output/damageprofiler/test/DNA_composition_sample.txt
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/editDistance.txt
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
- path: output/damageprofiler/test/Length_plot_combined_data.svg
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/lgdistribution.txt
md5sum: df2e19195185ea9ee05e8e84b2948f36
- path: output/damageprofiler/test/misincorporation.txt
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
- name: damageprofiler_specieslist
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 02:58:40 -05:00
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
fix: reduce number of required input files for damage profiler (#612) * Reduce number of required input files for damage profiler * Remove rebugging * Add optional species list file. * Working pending updated test-dataset update * Add genome header to config
2021-10-20 04:02:30 -04:00
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/chr22/3p_freq_misincorporations.txt
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
- path: output/damageprofiler/test/chr22/3pGtoA_freq.txt
md5sum: 61c903b1504ed7d7182570dfc75e4498
- path: output/damageprofiler/test/chr22/5pCtoT_freq.txt
md5sum: 15a75b60ee519b61ce04a83fe3afe855
- path: output/damageprofiler/test/chr22/5p_freq_misincorporations.txt
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
- path: output/damageprofiler/test/chr22/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/chr22/DamagePlot.pdf
- path: output/damageprofiler/test/chr22/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/chr22/dmgprof.json
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
- path: output/damageprofiler/test/chr22/DNA_comp_genome.txt
md5sum: fea48af1ecf491b439d36d4a919473df
- path: output/damageprofiler/test/chr22/DNA_composition_sample.txt
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
- path: output/damageprofiler/test/chr22/edit_distance.pdf
- path: output/damageprofiler/test/chr22/edit_distance.svg
- path: output/damageprofiler/test/chr22/editDistance.txt
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
- path: output/damageprofiler/test/chr22/Length_plot_combined_data.svg
- path: output/damageprofiler/test/chr22/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/chr22/Length_plot.pdf
- path: output/damageprofiler/test/chr22/lgdistribution.txt
md5sum: df2e19195185ea9ee05e8e84b2948f36
- path: output/damageprofiler/test/chr22/misincorporation.txt
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
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