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

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add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- name: pirate test_pirate
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/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/pirate/nextflow.config
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
tags:
- pirate
files:
- path: output/pirate/results/PIRATE.gene_families.ordered.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["allele_name"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/PIRATE.gene_families.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["allele_name"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/PIRATE.genomes_per_allele.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0197"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/PIRATE.log
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["PIRATE input options"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/PIRATE.pangenome_summary.txt
md5sum: 4551c291bc06b21f984f25c09329ed7d
- path: output/pirate/results/PIRATE.unique_alleles.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["allele_name"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/binary_presence_absence.fasta
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/binary_presence_absence.nwk
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: 1fcf7434911bbab39b74791259f1f989
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/cluster_alleles.tab
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0001"]
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
- path: output/pirate/results/co-ords/test1.co-ords.tab
md5sum: f1e75c045b35bae260dadb1a2f000dfa
- path: output/pirate/results/co-ords/test2.co-ords.tab
md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
- path: output/pirate/results/co-ords/test3.co-ords.tab
md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/genome2loci.tab
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/genome_list.txt
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: c19ac63da7949b15179f42093cbf95b8
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/link_clusters.log
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["parsing paralog file"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/loci_list.tab
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/loci_paralog_categories.tab
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
- path: output/pirate/results/modified_gffs/test1.gff
md5sum: 5dc220e472165c3b693e1017f38fc0e3
- path: output/pirate/results/modified_gffs/test2.gff
md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
- path: output/pirate/results/modified_gffs/test3.gff
md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pan_sequences.fasta
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: 0492833706f0f969b49a3555c16ec40d
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.connected_blocks.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["block_number"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.edges
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0259"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.gfa
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0001"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.order.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0172"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.reversed.tsv
md5sum: b2396ce09a6e4178761eca6dc7f4434f
- path: output/pirate/results/pangenome.syntenic_blocks.tsv
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0091"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome.temp
- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00081"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["test1_00242"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["chaos"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
md5sum: 6e483c773ed90bd50b33f2bd569343e4
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
- path: output/pirate/results/pangenome_log.txt
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["Creating pangenome on amino acid"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/paralog_clusters.tab
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["g0216"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/representative_sequences.faa
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["representative_genome"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/representative_sequences.ffn
Fix formatting in yaml files, add yamllint config (#1279) * fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 06:15:27 -05:00
contains: ["representative_genome"]
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 17:28:25 -04:00
- path: output/pirate/results/split_groups.log
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-24 22:11:04 -04:00
contains: ["g0"]
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