* first commit, added template files for new module
* created getpileupsummaries script, tests and both yml files
* fixed typo in meta.yml
* Update modules/gatk4/getpileupsummaries/meta.yml
changed gz_tbi to gz.tbi as suggested
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* feat(homer): Add initial makeTagDirectory
* feat(homer): Add initial findPeaks module
* feat(homer): Update with new options
See 1d30e2c21a
* fix(homer): Correct findpeaks process name
* fix(homer): Takes a bam file instead of bed
* feat(homer): Add initial makeTagDirectory test
* fix(homer): Hardcode genome and configureHomer
I'd like to modularize configureHomer, but I need to figure out how
exactly the genomes work.
* fix(homer): bam => bed
Bam requires samtools to be present, which it's not in this docker image
* feat(homer): Add initial configureHomer script
* ci(homer): Add initial test
* test(homer): Reproducible configuration workaround
- I can't run both tests(one file and two files) at the same time because it breaks
- I can't copy the genome stuff from the configurehomer module because it's read only
- So I can't make the makeTagDirectory module depend on configureHomer
* test(homer): Add placeholder annotatepeaks
The required inputs are necessarily required for all workflows from what
I've used, but I'll need to look at the actual docs
* test(homer): Add missing B.bed
* test(homer): Rename two => groseq
Then all of the various workflows that homer provides can be e2e tested
* feat(homer): Add initial makeUCSCfile module
* test(homer): Add start to makeUCSCfile testing
* chore(homer): Add various cleanups
* test(homer): Rewrite annotatepeaks
Not passing yet
* test(homer): Rewrite configurehomer
* test(homer): Rewrite findpeaks
Still failing
* test(homer): Rewrite makeucscfile
Not passing yet
* test(homer): Rewrite maketagdirectory
All homer modules now follow the new structure. Time to make them pass.
* test(homer): Fix typo for workflow name
* fix(homer): Use correct container
* fix(homer): Accept fasta in maketagdirectory
Apparently all of the homer stuff can just take any old fasta and you
don't need to configure the genome ahead of time with configureHomer
* test(homer): makeTagDirectory passes now
* fix(homer): Update containers in makeucscfile
* test(homer): Rewrite makeucscfile
Takes input from maketagdirectory which is how the module should be used
* fix(homer): Update makeUCSCFile bedgraph path
* test(homer): Update makeucscfile expected output
* fix(homer): Update containers in findpeaks
* fix(homer): Change findpeaks args
The user is just going to have to know what they're doing for now
* test(homer): findPeaks rewrite with tagDir input
* test(homer): Update expected files for findPeaks
And bump filters
* style: Appease editorconfig
* ci: Remove old workflow
* tests(homer): Add md5sums
* test(homer): Add meta test
* style(homer): Capitalize HOMER
* docs(homer): Add maketagdirectory meta.yml
* docs(homer): Add makeucscfile meta.yml
* docs(homer): Add findpeaks meta.yml
* test(homer): Update to new test data standards
* chore: Remove stuff that got revived in the rebase
* chore: software => modules
* test(homer): Update tags
* test(homer): Update annotatepeaks
* ci: Fix uploading of artifacts
GitHub actions doesn't like the / in the tags
* test(homer): Remove annotate md5sum
This is failing and breaking new tests
* test(homer): Use bams instead of beds
* test(homer): Fix meta maketagdirectory
* test(homer): Fix input in all tests
* test(homer): Move back to bed files
Forgot samtools isn't present
* chore(homer): Add TODOs for tests
* test(homer): Add bed format arg
* test(homer): Update md5sums
* test(homer): Fix tags tsvs
* style(homer): Appease nf-core linting
* docs(homer): Be in line with what is in the main.nf file
Co-authored-by: Kevin Menden <kevin.menden@live.com>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
Please enter the commit message for your changes. Lines starting
* adds expansionhunter module
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Initial draft [ci skip]
* trigger first test
* update output file path
* Tests passing
* finishing touches for meta.yml and update checksum
* tweak checksum
* add threads to the module
* skip version info for matching test md5sum [ci skip]
* Add ref fasta and finalize the module
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* draft for bcftools modules [ci skip]
* initial test for bcftools concat
* Update the params for testing
* fix tests
* Accomodate code review [ci skip]
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update the meta file and open PR for review
* Update the keyword
* Update the tags for module [ci skip[
* add threads
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add MALT with incomplete tests
* Parameter typo fix
* Clean up test yaml
* Finish MALT module prior UNZIP and MALT_BUILD modiules
* Add required modules for tests
* Sync test out with malt-build
* Fix input parameters in tests based on final build module
* Update modules/malt/run/meta.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add sampe
* Fix container paths
* Update based on code review from @grst
* Update input docs
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add bwa/aln module
* Also output reads as required with SAI
* Add bwa samse
* Fix container paths
* remove TODO comment
* Updated based on code from from @grst on bwa/sampe
* Clarify output docs
* Specify more guidelines on input channels
* Linting
* Updates based on code review
* Update README.md
* Fix broken sentence
* Add unzip module
* Remove missing TODOs update mtea
* Apply changes after code-review from @grst
* Account for user trying to supply two input archives
* Remove debugging test
* Update modules/unzip/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Correct output path
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Updated the version of STAR in align and genomegenerate modules
* Changes in test.yml
* Changes in test.yml
* Added module arriba
* Changes in test configs
* Added module Arriba for fusion detection
* Fixed review comments
* Added an output option for discarded fusions
* Resolved some conflits
* conflicts
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update README
* Rename pytest_software.yml to pytest_modules.yml
* Rename main software directory to modules
* Remove deprecated modules
* Rename tests software to modules
* Replace paths for tests in pytest_modules.yml
* Replace software with modules in Github Actions
* Replace software with modules in main.nf tests
* Rename software to modules in test.yml
* testing works but need to fix paths and add exclude list
* edited meta file and removed TODOs
* left over TODOs
* test passed, final push
* resolving initial comments
* Update software/delly/call/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* created templates
* updated functions.nf to the one on dev
* Created test main
* Fasta added and docker, conda, singularity passing
* Fixed output version lint
* Created module template (#558)
* Created meta and implemented main (#558)
* Conda test and lint passing (#558)
* Updated functions.nf to the one on dev (#558)
* Update software/lofreq/filter/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add software/pairtools
* create a branch for pairtools/select
* fix the different output of conda and docker.
* rmove the md5sum for gzip files.
* Update software/pairtools/select/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* update test file and documentation.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* 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
* 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
* Added seqtk/subseq and checking for seed in seqtk/sample
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Update samtools from 1.10 to 1.12 (#530)
* feat: remove social preview image to use GitHub OpenGraph
* feat: update samtools from 1.10 to 1.12
* fix: CI tests
* fix: add meta.yml file for samtools/merge
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update software/samtools/merge/meta.yml
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* 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
* Added seqtk/subseq and checking for seed in seqtk/sample
* 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
* Separate authors in software/seqtk/sample/meta.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Align commans in output channesl software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define prefix in software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Use prefix in output file name software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Define suffix in options in tests/software/seqtk/subseq/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change output file name in tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Remove a to-do point from tests/software/seqtk/subseq/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added --no-name into gzip commands
* Replaced functions.nf in seqtk/subseq
* Refreshed tests for sample and subseq
* Corrected paired-end test and YAML description for sample
Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add software/pairtools
* create a branch for pairtools/restrict
* fix the different output of conda and docker
* remove customized code.
* add newline to Frag.bed file.
* change the folder of frag.bed.
* change \n to \r\n
* Remove work.frag.bed
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
* New last/mafconvert module to convert MAF alignments.
The `maf-convert` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reads alignmnts in [MAF](https://genome-asia.ucsc.edu/FAQ/FAQformat.html#format5)
format and converts them in another format (axt, blast, blasttab, chain,
gff, html, psl, sam, tab).
This new module is part of the work described in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency.
We will upgrade it later.
* Delete white space.
* Update the function.nf file to the dev version.
The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
filters alignments in a MAF file to remove those with too many masked
(lower-case) positions compared with their score.
As other filter modules like `last/split`, its output file risks to
overwrite its input file as their names are constructed from the sample
ID when multiple filters are chained in the pipeline. I added a check
that gives a clearer error message in this case. Please let me know
what you think about; I can add this test to the existing LAST modules
as well.
This new module is part of the work discribed in Issue #464. During this
development, we fix the version of LAST to 1219 to ensure consistency.
We will upgrade it later.
* New last/dotplot module for pairwise similarity plots
The `last-dotplot` tool takes a pairwise alignment in
[MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format,
possibly compressed with gzip, or in a tabular format produced by the
`maf-convert` tool, and produces a similarity dot-plot of the two
sequences in one of the graphical formats supported by the Python
Imaging Library.
A the tool guesses the output format by the file extension of the file,
which is constructed by the module at run time, I have used the `args2`
option to convey this information to the module.
This new module is part of the work described in Issue #464. During
this development, we fix the version of LAST to 1219 to ensure
consistency (hence please ignore lint's version warning).
* Update the functions.nf file to the dev branch.
https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
* add software/pairtools
* create a branch for pairtools/sort
* fix the different output of conda and docker.
* remove customized code.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
