Abhinav Sharma
15fd90ffe8
Add phyloflash module ( #786 )
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* initial stubs [ci skip]
* remove comments and add main command [ci skip]
* design iteration [ci skip]
* add new standard functions.nf [ci skip]
* update the version string [ci skip]
* accomodate the db stubs and single/double ends [ci skip]
* add FIXME for missing info [ci skip]
* Accomodate the results folder [ci skip]
* Update main.nf
* Apply suggestions from code review
* Update main.nf
* Apply suggestions from code review
* Add version file to stubs [ci skip]
* Tweak the output dir pattern [ci skip]
* Update modules/phyloflash/main.nf
* Update modules/phyloflash/main.nf
* Update modules/phyloflash/main.nf
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-21 19:43:58 +00:00
Sébastien Guizard
c25c3fe466
Update: uLTRA ( #1081 )
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* 👌 IMPROVE: Update .gitignore
* 📦 Add ultra module
* 👌 IMPROVE: Update test input
* 👌 IMPROVE: Update and clean code
- Update to last versions.yml file
- Update meta.yml
- Correct typos
* 👌 IMPROVE: Update output channels + Rename following subtool
* 👌 IMPROVE: Remove old ultre files
* 👌 IMPROVE: Update of pytest_modules.yml
* 👌 IMPROVE: Update test.yml
* 👌 IMPROVE: Keep md5sum as much as possible
* 👌 IMPROVE: Remove old ultra files
* 👌 IMPROVE: Update of pytest_modules.yml
* 👌 IMPROVE: Update test.yml
* 👌 IMPROVE: Keep md5sum as much as possible
* 🐛 Fix: add unsaved modifications
* 🐛 FIX: Remove one inconstant md5sum
* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}
* 🐛 FIX: Remove md5sums for pickle files (not constant).
* Update modules/ultra/pipeline/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/ultra/pipeline/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: update output directory, update meta.yml
* 👌 IMPROVE: Use modules to gunzip and sort gtf
* 🐛 FIX: Set up channel correctly
* 👌 IMPROVE: Remove pickles files and databases
Those data might be useful in a debugging purpose.
* Apply suggestions from code review
* Update main.nf
* 🐛 FIX: Update uLTRA to version 0.0.4.1 + remove $(pwd)
* 👌 IMPROVE: Sort tags in test.yml
* align order of input between main.nf and meta.yml. Add ksahlin as co-author (he did update his package to overcome the pwd-problem
* Update main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 13:00:53 +00:00
James A. Fellows Yates
d30bf235b1
update: gunzip to include meta input tuple ( #1082 )
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* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add bamUtil trimBam
* Update modules/bamutil/trimbam/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/bamutil/trimbam/main.nf
* Changes after code-review
* YAML lint
* update: add (optional) meta to input tuple
* YAML linting
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-21 12:41:03 +00:00
Robert A. Petit III
29c669766d
add bakta module ( #1085 )
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* add bakta module
* Update main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:17:25 +00:00
Robert A. Petit III
5ebe62612c
add ectyper module ( #948 )
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* add ectyper module
* fix-lint
* try zcat
* Update main.nf
* fix lint
* Update main.nf
* Apply suggestions from code review
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
* Update main.nf
* pass lint
* Update main.nf
* fix lint
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:14:02 +00:00
Maxime Borry
72c94dbed9
Add new module: Das Tool ( #1004 )
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* add pydamage module
* remove TODOs
* split module by subcommands
* update version parsing
* remove forgotten TODOs
* update module names
* remove old holistic module
* Update modules/pydamage/analyze/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add keywords
* update resource requirement
* Update modules/pydamage/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pydamage/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* merge from upstream
* update pydamage from upstream
* add freebayes
* update pydamage test from upstream
* fix meta.yml
* update functions.nf
* update test.yml
* update version parsing
* update version parsing
* fix indentation
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add bed test
* add metabat2 module
* only freebayes
* remove metabat2
* update md5sum because of vcf including date of the day
* add keyword
* rescue conflicted files
* attempt to fix ECLint
* add pytest workflow for metabat
* remove -
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs/outpus
* remove trailing whitespace
* compressing and removing not reproducible md5sums
* follow symlinks while decompressing
* add dastool/scaffolds2bin
* add dastool
* remove non reproducible md5sum check for compressed files
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* split tests
* export env variable
* remove metabat2 from PR
* fix linting errors
* remove traling whitespace
* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* answer PR comments and switch to bgzip
* PR review updates
* update from PR review
* update test files
* add bacillus fragilis alignments
* switch tests to bacillus fragilis
* add string check
* update test string
* add pr comment answer
* last fixes for PR review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 08:33:29 +01:00
FriederikeHanssen
19035c99d1
Add thread option to samtools modules ( #1069 )
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* add thread option to samtools modules
* fix tests
* fix tests
* fix tests
* Fix naming to fix tests
* cpus-1 to account for mainthread
* remove thread in ampliconclip, docu doesn't report this param
* add -1 to all other applicable samtools modules
* Update samtools version
* Update checksums
* retrigger GHA after update
* Update modules/samtools/fastq/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/fixmate/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/flagstat/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/index/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/merge/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/stats/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Update modules/samtools/view/main.nf
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
* Fix md5sum fixmate
* Fix md5sums
* sth funny with the fixmate checksums
* more md5sums updates
Co-authored-by: Patrick Hüther <patrick.huether@gmail.com>
2021-11-18 22:24:47 +01:00
Jose Espinosa-Carrasco
4e5b6ed843
Fix picard markduplicates ( #1084 )
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* Fix picard/markduplicates with new options syntax
* Delete md5sum for bam files and add contains for metrics.txt
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-18 21:54:14 +01:00
praveenraj2018
43a1c1c6d1
Update in GATK4 variantfiltration: Added vcf_index to vcf tuple; output to vcf.gz format. ( #1083 )
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* Added vcf_index to vcf tuple; output to vcf.gz format.
* Fix: extra new line in meta.yml.
* addressed review feedback
* fix: editorconfig error
* fix: gatk memory flag
* fix: editorconfig error
* fix: Indentation
fix: Indentation
* Fix: lint editorconfig error
Removed one extra space
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-18 21:47:40 +01:00
Robert A. Petit III
f052dc445c
use underscores in anchors and references ( #1080 )
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* use underscores in anchors and references
* Dummy change to trigger CI
* use dev branch
* underscore anchor
2021-11-18 18:09:09 +00:00
GCJMackenzie
5b975cc20d
Add gatk somatic paired calling subworkflow ( #1067 )
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* initial commit to setup branch
* workflow finished
* Update nextflow.config
* tumour to tumor, getpileup passed as nomral and tumor
* paired_somatic renamed to tumor_normal_somatic
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* updated index names in meta.yml
* changed index file names in main script and test
* Apply suggestions from code review
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Apply suggestions from code review
* fixed bug from changes
* Apply suggestions from code review
* tests should now work after the yml update
* Update pytest_modules.yml
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-11-17 11:34:07 +01:00
GCJMackenzie
071b1d50a8
Add gatk somatic tumour calling subworkflow ( #1064 )
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* initial commit to set up new branch
* save changes to checkout
* workflow working, still needs test.yml and meta.yml, also fix versions file
* subworkflow finished
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* Update pytest_subworkflows.yml
* fix config subworkflow name
* Update main.nf
* Update pytest_subworkflows.yml
* fixed md5sum issue likely caused by gatk version update
* tumour changed to tumor
* old dir deleted
* Comments added to explain use of placeholders '[]'
* updated index names, input channel renamed to input
* Apply suggestions from code review
* updated to perform new subworkflow testing
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-17 11:07:17 +01:00
praveenraj2018
691feeafdc
GATK4 SplitNCigarReads: fasta_fai_dict tuple is now split into separate input channels ( #1076 )
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* fasta_fai_dict tuple is now split into separate input channels
* fix: lint errors
* fix: pytest errors
* Update modules/gatk4/splitncigarreads/meta.yml
* Update modules/gatk4/splitncigarreads/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-11-16 15:09:30 +01:00
Robert A. Petit III
bc8899f1bf
[fix] hicap module allow optional outputs ( #937 )
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* make hicap outputs optional
* update test data
* typo
* Update main.nf
* use mkfifo
* Update main.nf
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-16 09:23:07 +00:00
Sateesh
d5f6985607
add new nucmer module ( #945 )
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* add new nucmer module
* Apply suggestions from code review
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update tests with file produced by input
* Update main.nf
* Update meta.yml
Co-authored-by: Michael Cipriano <mcipriano@gmail.com>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 22:05:34 +00:00
JIANHONG OU
52c541b080
Cooler cload ( #634 )
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* rebuild cooler cload.
* update test file path of cload.
* add pytest for cload
* update to version.yml
* update the test data path
* Update tests/modules/cooler/cload/main.nf
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* Update modules/cooler/cload/main.nf
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* Update tests/config/test_data.config
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
* Update main.nf
Remove a lonely curly bracket.
* Update test.yml
Updated with new workflows.
* update the test files
* merge the conflicts.
* update the test.yml
* update for change of cooler/dump
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 21:43:55 +00:00
Robert A. Petit III
c2bba7a65d
add clonalframeml module ( #974 )
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* add clonalframeml module
* Update main.nf
* try recommended gzip
* Update main.nf
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 19:43:53 +00:00
tamara-hodgetts
13b8a16f4a
Add module get_chrom_sizes ( #1063 )
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* hifiasm copied from fastqc
* hifiasm tests init from fastqc
* meta.yml init; test.yml and main.nf for printing version
* Add hifiasm version printing
* Removed spaced on an empty line
* Reverted hifiasm from main
* init getchromsizes
* add tests for getchromsizes
* Included meta.yml
* removed whitespace
* Moved getchromsizes to custom folder
* Update modules/custom/getchromsizes/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 19:22:12 +00:00
Robert A. Petit III
2294ff7826
add ncbi-genome-download module ( #980 )
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* add ncbi-genome-download module
* Update modules/ncbigenomedownload/main.nf
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:32:53 +00:00
SusiJo
ad46010385
Added new module csvtk/split ( #1014 )
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* added module csvtk/split
* removed todo statement
* adjusted meta map names
* changed tests to use generic input files
* added module in pytest
* updated test-data paths
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:29:55 +00:00
Edmund Miller
2af071ed0d
Fix subworkflows seperate from modules ( #933 )
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* ci: Remove pytest_subworkflows
* ci(bam_sort_samtools): Depend on paths-filter instead of pytest-workflow
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* ci: Revert back to one job branch
* ci(align_bowtie2): Run tests that depend on bam_sort_samtools
* ci: Fix anchor not being created yet
* ci: Update sra_fastq tags and pytest_modules
* fix(bam_sort_samtools): Update nextflow.config with params
* test(subworkflows): Update gatk_create_som_pon tags
* ci: Point to subworkflow_hacks branch of nf-core tools
Co-authored-by: Harshil Patel <drpatelhh@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-11-15 18:18:46 +00:00
avantonder
527ccdb419
Add Miniasm module ( #962 )
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* add racon
* add miniasm module
* edit miniasm module
* edit miniasm module
* Update tests/modules/racon/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update tests/modules/racon/test.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update modules/miniasm/meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update main.nf
Add some spaces.
* Update meta.yml
Correct DOI
* Update main.nf
* Apply suggestions from code review
* Update tests/modules/miniasm/test.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:50:56 +00:00
mjakobs
466b964b37
add Kronatools KTImportTaxonomy ( #928 )
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* created and initialised krona module
* Added kronatools/ktimporttaxonomy module
* removing previous redundant work
* added contains info for html
* edited contains in test.yml
* Update get versions
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* remove old syntax
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* rewording module description
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* added detailed keywords
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update syntax and tool version
* fixed meta.yml issues
* remove contains line from test.yml
* re-wrote module after nf-core/tools update - should work now
* removed md5
* Update modules/kronatools/ktimporttaxonomy/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* update meta save
* removed typo
* double quotes to single quotes around html
* re-ran test, which updated md5
* removed md5
* 'classifier' removed to fix linting
* update version
* removed erroneous ktimporttaxonomy2
* Updated input to include meta and database
* fixed tab issues in yaml
* added `contains` to test.yml
* edited `contains` in test.yml
* trying another `contains`
* retrying `contains`
* contains with extra line
* removed classifier from tag
* Apply suggestions from code review
* Update meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
avantonder
8d9e8ae839
Add Medaka module ( #992 )
...
* add racon
* add medaka module
* add medaka module
* add medaka module
* add medaka module
* add medaka module
* add medaka module
* Indentation
* Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update main.nf
* Update main.nf
* Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00
JIANHONG OU
4398056204
Macs2 calllpeak ( #1038 )
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* Add tests and yml file for macs2/callpeak
* add format option for macs2
* update macs2/callpeak to accept format argument
* update test.yml
* update the container version.
* try to fix the issue in conda container.
* Update conda and containers
* Going back to previous container versions
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-11-15 18:17:40 +01:00
Maxime U. Garcia
3426834744
feat: fastaidx -> fai ( #1073 )
2021-11-15 18:03:02 +01:00
Maxime U. Garcia
5b1ce484b9
feat: _idx -> _tbi ( #1074 )
...
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:49:20 +01:00
James A. Fellows Yates
632587a7fc
Add bamutil/trimbam ( #1060 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add bamUtil trimBam
* Update modules/bamutil/trimbam/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/bamutil/trimbam/main.nf
* Changes after code-review
* YAML lint
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-11-15 16:44:12 +00:00
louperelo
eff515891d
new module fargene ( #1068 )
...
* new module fargene
* Update main.nf
* Update modules/fargene/main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 16:42:48 +00:00
JIANHONG OU
7ad42eae1b
Cooler zoomify ( #514 )
...
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/zoomify
* Apply suggestions from code review
* update functions.nf to new version.
* update the test file to test-datasets.
* update the test method of zoomify
* update dump test file.
* update version.txt to version.yml
* Update modules/cooler/dump/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix the output bug of versions update to pytest_modules.yml
* update the test file path and fix the output versions.
* Update modules/cooler/dump/main.nf
* indent
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 17:18:02 +01:00
mjakobs
f93c2f2604
add Krona_db module ( #995 )
...
* add Krona_db module
* removed md5 sum
* Update tests/modules/kronatools/kronadb/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* added input information
* removed trailing white spaces
* changed krona version to 2.7.1
* Apply suggestions from code review
* Update modules/kronatools/kronadb/meta.yml
* Update modules/kronatools/kronadb/main.nf
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
2021-11-15 16:01:46 +00:00
Sébastien Guizard
4a9bfec61d
New module: Ultra ( #871 )
...
* 👌 IMPROVE: Update .gitignore
* 📦 Add ultra module
* 👌 IMPROVE: Update test input
* 👌 IMPROVE: Update and clean code
- Update to last versions.yml file
- Update meta.yml
- Correct typos
* 👌 IMPROVE: Update output channels + Rename following subtool
* 👌 IMPROVE: Remove old ultre files
* 👌 IMPROVE: Update of pytest_modules.yml
* 👌 IMPROVE: Update test.yml
* 👌 IMPROVE: Keep md5sum as much as possible
* 👌 IMPROVE: Remove old ultra files
* 👌 IMPROVE: Update of pytest_modules.yml
* 👌 IMPROVE: Update test.yml
* 👌 IMPROVE: Keep md5sum as much as possible
* 🐛 Fix: add unsaved modifications
* 🐛 FIX: Remove one inconstant md5sum
* 🐛 FIX: Grab software name using ${getSoftwareName(task.process)}
* 🐛 FIX: Remove md5sums for pickle files (not constant).
* Update modules/ultra/pipeline/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update modules/ultra/pipeline/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: update output directory, update meta.yml
* 👌 IMPROVE: Use modules to gunzip and sort gtf
* 🐛 FIX: Set up channel correctly
* 👌 IMPROVE: Remove pickles files and databases
Those data might be useful in a debugging purpose.
* Apply suggestions from code review
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 15:57:58 +00:00
Michael J Cipriano
0754d49db8
Initial commit mummer module ( #940 )
2021-11-15 16:53:41 +01:00
santiagorevale
1a4c7cec1b
New modules added: issues #200 and #310 ( #884 )
...
* New modules added: issues #200 and #310
* Update main.nf
* Update meta.yml
* Update tests/modules/gatk4/genotypegvcfs/main.nf
* Apply suggestions from code review
* Update main.nf
* Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config
* Some minor changes on one of the test files I forgot to include
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
JIANHONG OU
a6ca2b006b
Cooler merge ( #515 )
...
* add software/cooler
* fix the wrong files uploaded.
* create a branch for cooler/merge
* remove the bin_size from metadata.
* update the test_data to test-datasets
* update pytest_modules.yml
* update the test file from single input file to two input file.
update the output file from hdf5 to bedpe.
* update the version.txt to version.yml and functions.nf
* change version.yml to versions
* update the test file path and fix the output versions.
* Update meta.yml
Correct "version" to "versions"
* Update main.nf
Fix typo
* Update main.nf
Remove some spaces
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-15 15:18:43 +00:00
Robert A. Petit III
b5b3ff16ce
add module for fastq-scan ( #935 )
...
* add module for fastq-scan
* change fastq to reads
* remove uncompressed support
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:41:36 +01:00
Robert A. Petit III
7be60774b6
add module for tbprofiler ( #947 )
...
* add module for tbprofiler
* Update test.yml
* Update meta.yml
Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:35:55 +01:00
James A. Fellows Yates
2c3c87a10f
Add leehom module ( #1052 )
...
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* feat: add megahit module, currently decompressed output
* Update main.nf
* Update tests/modules/megahit/test.yml
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* feat: compress all outputs, remove md5sums due to gz stochasicity
* fix: wrong conda channel for pigz
* fix: broken singleend tests and update meta.yml
* Missed one
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: pigz formatting
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Apply suggestions from code review
* Add leeHom module
* Update modules/leehom/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update modules/leehom/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update modules/leehom/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update modules/leehom/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 15:26:06 +01:00
Benjamin Wingfield
b012b349c1
New module: plink2/vcf ( #1006 )
...
* implement plink2 VCF import
* fix yaml indentation
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 13:55:18 +00:00
Ilya Pletenev
c48244b677
Add new module 'ataqv/ataqv' ( #998 )
...
* Add new module 'ataqv/ataqv'
* Update main.nf
* Update main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
Daniel Straub
661bdb645e
Change Spades input ( #1039 )
...
* Change spades module
* correct meta map description
* adjust memory handling
* remove trailing whitespace
* fix hmm input
* Update modules/spades/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:53:07 +00:00
Daniel Straub
171a2a2dbf
Unicycler with long read input ( #1041 )
...
* Unicycler with long read input
* tests and md5sums
* remove unstable md5sums
* Update modules/unicycler/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:48:56 +00:00
JIANHONG OU
9475960928
Bwa index ( #1040 )
...
* fix a bug that the prefix is not handled by index.
* build the test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 11:26:01 +00:00
alexandregilardet
94851901d5
add new module pmdtools/filter #847 ( #963 )
...
* commit but won't be used because pmdtools should have a submodule
* added submodule pmdtools/filter
* removed pmdtools module created before deciding to design two submodules
* oops forgot to remove a TODO
* removed white space meta.yml, removed v in version and manually added submodule /filter to test
* Update pytest_modules.yml
* Update main.nf
added split_cpus for multi-tools module resources
* Update test.yml
added .pmd extension to match modules/ main.nf
* Update test.yml
update md5sum
* Update singularity and docker build in main.nf
From build 4 to 5 in order to match the conda one
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pmdtools/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update main.nf adding samtools version
we need both pmdtools and samtools versions
* Update main.nf remove .pmd extension
* Update test.yml md5sum
Because file extension changed
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
Sébastien Guizard
001d5071c2
Update: gstama/collapse ( #1057 )
...
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Remove junk files
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: Re add 10000 data test
* 👌 IMPROVE: Add some pbindex
* 🐛 FIX: Add pbi extension to files
* 📦 NEW: Add galgal6 chr30 test data
* 📦 NEW: Add gd-tama module
* 🐛 FIX (TEMP): Update singularity container address
* 📦 NEW: Add bamtools module
* 📦 NEW: Rewrite and rename module (gstama => gstama/collapse)
* 👌 IMPROVE: ignore test data
* 👌 IMPROVE: Update output
* 👌 IMPROVE: Add channel for publishing tama's metadata outputs
* 👌 IMPROVE: Update process label
* 🐛 FIX: Use depot.galxyproject.org url for singularity
* 👌 IMPROVE: autoselect running mode
* 🐛 FIX: correct gstama collapse bash test
* 👌 IMPROVE: Update to last templates version
* 👌 IMPROVE: Update tama package and label
* 👌 IMPROVE: Final version of test datasets config
* 👌 IMPROVE: Remove useless index + Fix Typos
* 👌 IMPROVE: Update test
* 👌 IMPROVE: delete unnecessary files
* 👌 IMPROVE: Update + clean
- Remove unnecessary files
- Update to new versions.yml file
- Better output channels
* 👌 IMPROVE: Update meta.yml and output channels
* 👌 IMPROVE: Remove useless files
* 👌 IMPROVE: Remove automatic MODE setup
* 👌 IMPROVE: Applied @jfy133 code modification suggestions
* Update modules/gstama/collapse/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* 🐛 FIX: Add missing fasta option in meta.yml
* 🐛 FIX: Fix typo
* 🐛 FIX: Update package version
* Update main.nf
* Update meta.yml
* Update modules/gstama/collapse/meta.yml
* Apply suggestions from code review
* Update tests/modules/gstama/collapse/main.nf
* Update main.nf
* 👌 IMPROVE: Update to gs-tama 1.0.3
* Update modules/gstama/collapse/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:57:55 +00:00
Sébastien Guizard
ec15d0f9fd
Update module: pbccs ( #1018 )
...
* 📦 NEW: First commit of pbccs module
* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)
* 👌 IMPROVE: Move .pbi output into report channel
* 🐛 FIX: Correct code after --rq option removal from command line module
- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums
* 🐛 FIX: Repair additionnal option usage
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: CCS is run in parallel with --chunk option
* 👌 IMPROVE: Add Pbindex in bam ouput channel
* 👌 IMPROVE: Change label to process_low
* 👌 IMPROVE: Define reports files names + add json version of txt report
* 🐛 FIX: Add missing backslashes
* 🐛 FIX: Add missing gz extension
* 🐛 FIX: update ouput channel
* 🐛 FIX: output file name
* 👌 IMPROVE: .gitignore
* 👌 IMPROVE: Update function.nf to last version
* 👌 IMPROVE: Update saveAs in main.nf
* 👌 IMPROVE: Add pbccs module
* 🐛 FIX: Fix Broken test
* 👌 IMPROVE: Update test_data.config
* 🐛 FIX: Fix test
* 👌 IMPROVE: Update path of test dataset files
* 👌 IMPROVE: Remove useless index + Fix Typos
* 📦 NEW: First commit of pbccs module
* 👌 IMPROVE: Remove option from command + rename output (ccs -> bam)
* 👌 IMPROVE: Move .pbi output into report channel
* 🐛 FIX: Correct code after --rq option removal from command line module
- module main.nf: Remove ramaining rq input channel
- Test main.nf: Transfert rq into addParams
- Test test.yml: Update md5sums
* 🐛 FIX: Repair additionnal option usage
* 👌 IMPROVE: Add some pacbio test files
* 🐛 FIX: Add Pacbio index to test_data.config
* 👌 IMPROVE: CCS is run in parallel with --chunk option
* 👌 IMPROVE: Add Pbindex in bam ouput channel
* 👌 IMPROVE: Change label to process_low
* 👌 IMPROVE: Define reports files names + add json version of txt report
* 🐛 FIX: Add missing backslashes
* 🐛 FIX: Add missing gz extension
* 🐛 FIX: update ouput channel
* 🐛 FIX: output file name
* 👌 IMPROVE: .gitignore
* 👌 IMPROVE: Update function.nf to last version
* 👌 IMPROVE: Update saveAs in main.nf
* 👌 IMPROVE: Add pbccs module
* 🐛 FIX: Fix Broken test
* 👌 IMPROVE: Update test_data.config
* 🐛 FIX: Fix test
* 👌 IMPROVE: Update path of test dataset files
* 👌 IMPROVE: Remove useless index + Fix Typos
* 🐛 FIX: fill contains args
* 👌 IMPROVE: One output => One Channel
* 👌 IMPROVE: One input => One channel
* 🐛 FIX: Update tests
* 🐛 FIX: Remove TODOs from test.yaml
* 👌 IMPROVE: Revert and keep bam and pbi together
* 🐛 FIX: Remove old rq input from meta.yml
* 👌 IMPROVE: Update test to match input channels
* 👌 IMPROVE: use prefix for for output file name
* 👌 IMPROVE: Update to new versions.yml
* 👌 IMPROVE: Update pbccs from v6.0.0 to v6.0.2
* 👌 IMPROVE: Keep track of the former sample id in meta
* Update modules/pbccs/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* 👌 IMPROVE: remove former_id from meta
* 👌 IMPROVE: Use chunk number in output filename
* 🐛 FIX: Update meta.yml
* 🐛 FIX: Update reports filenames with chunk number.
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-11 14:19:26 +00:00
Maxime U. Garcia
3b600af50e
feat: update gatk4 from 4.2.0.0 to 4.2.3.0 ( #1059 )
...
* feat: update gatk4 from 4.2.0.0 to 4.2.3.0
* update md5checksum
* commit all files
* actually checksum was good, but I suspect something fishy with the tests
2021-11-11 08:58:59 +01:00
Robert A. Petit III
4bd530135f
add ngmaster module ( #1024 )
...
* add ngmaster module
* add docker container
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 11:25:50 -07:00
Maxime Borry
56d5eb9834
Add Bacillus fragilis alignments to test_data.config ( #1054 )
...
* add pydamage module
* remove TODOs
* split module by subcommands
* update version parsing
* remove forgotten TODOs
* update module names
* remove old holistic module
* Update modules/pydamage/analyze/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add keywords
* update resource requirement
* Update modules/pydamage/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pydamage/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* merge from upstream
* update pydamage from upstream
* add freebayes
* update pydamage test from upstream
* fix meta.yml
* update functions.nf
* update test.yml
* update version parsing
* update version parsing
* fix indentation
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add bed test
* add metabat2 module
* only freebayes
* remove metabat2
* update md5sum because of vcf including date of the day
* add keyword
* rescue conflicted files
* attempt to fix ECLint
* add pytest workflow for metabat
* remove -
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs/outpus
* remove trailing whitespace
* compressing and removing not reproducible md5sums
* follow symlinks while decompressing
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* split tests
* export env variable
* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* answer PR comments and switch to bgzip
* add bacillus fragilis alignments
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 17:40:07 +01:00
Maxime U. Garcia
64006e239a
fix: actually do the tests for multiple files ( #1058 )
2021-11-10 16:26:34 +01:00
