* New module last/mafswap to reorder sequences in alignments
The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
reorders sequences in alignment files in Multiple Alignment Format.
When run without command-line arguments, it will swap the target and the
query sequences. This is useful when turning a many-to-many alignment
into a many-to-one and then a one-to-one alignment in conjunction with
the `last-split` command (split, swap, split and swap again).
The LAST aligner outputs MAF files, but other tools also use this
format. As MAF files can be very large (up to hundreds of gigabytes),
the module expects its input to be compressed with gzip and will
compress its output.
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 ignore lint's version warning).
* Update MD5 sum.
Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of
an empty file compressed with `gzip --no-name`… This happened
because I forgot to update the config file after correcting the
module… sorry !
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Change name as suggested in pull request.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* New last/train module to train alignment parameters.
The last-train command creates a parameter file that
will be used by last/lastal module for sequence alignment.
It takes indexed sequences and query sequences as input
and we use the metadata of both to create an id of the
parameter output file.
Submission of the LAST modules is discussed in more
details in the issue #464. For consistancy, we use LAST
version 1219 for this whole development and will upgrade later.
* Corrected files according to the nf-core v1.14 standards.
* Fixed function.nf file for the last-train module.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Find index name.
* Correct after the input channels were changed.
* Use double underscore as a name separator.
Single underscores can happen in ids, therefore, we would like to keep two underscores.
* Remove extra spaces.
* Fixed the passing of the "score matrix" line.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/last/train/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Running pytest with `--tag fastqc_single_end` does not work (it runs zero tests), as it appears that the tag name was changed to `fastqc` during the transition from underscores to slashes.
* added intervallisttools module
* add intervallisttools module
* arguments are now supplied using options.args
* removed java heapsize settings
* changes in main.nf and it is tested
* comment added
* Update software/gatk4/intervallisttools/meta.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* Update tests/software/gatk4/intervallisttools/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* review comment on tags in bedtointerval
* modified the test to get input from bedtointerval module
* Update software/gatk4/intervallisttools/meta.yml
* Apply suggestions from code review
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Apply suggestions from code review
* Update tests/config/pytest_software.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Apply suggestions from code review
* Apply suggestions from code review
Co-authored-by: @praveenraj2018 <praveen.raj.somarajan@ki.se>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* output constant sites as a val as well as a file so it can be passed into iqtree
* Using an env variable because that's far safer!
* Update software/snpsites/main.nf
* remove hardcoded param that should be a user option
* Update software/snpsites/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Bump pangolin version
* Add nextclade to software list
* Add nextclade module
* Update md5sum for Pangolin due to version bump
* Adding some URL to meta.yml
* Adding new line at end of file
Co-authored-by: JoseEspinosa <kadomu@gmail.com>
* New last/lastdb module to index sequences before alignment.
The `lastdb` command creates a sequence index for the LAST aligner
(https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ
format, and compression is handled automagically. DNA or protein
sequences can be indexed.
The sequence index is a collection of files sharing the same basename.
This module sets the basename to the sample identifier (`$meta.id`) and
creates the index in a directory always called `lastdb`. The module's
output channel then conveys a copy of the metadata and the path to the
`lastdb` directory.
Other modules will follow (see Issue #464). The LAST aligner can align
proteins to proteins, DNA to DNA and can translate DNA align to
proteins.
* Remove trailing whitespace.
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update as suggested in PR.
* Attempt to pass linting.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update README to include some git best practices
* correct linting errors
* extra info about returning to master and deleting the branch
* use rebase
* stress importance of rebase
* Update README to include some git best practices
* correct linting errors
* extra info about returning to master and deleting the branch
* Changed position of git commands
* move later git commands down the action list
* Basic kb-python count functionality for scRNA-seq quantification working.
* Added tests and test data for workflow kite.
* Removed trailing whitespace
* Changed output channels to tuples with meta
Based on suggestions by @KevinMenden.
* Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message.
* Update software/kallistobustools/count/main.nf
@KevinMenden fixed wrong path definition
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Increased version of kb-python
* Updated tests with raw links.
* Fixed subtool referencing: kallistobustools/count
* Added newline
* Update software/kallistobustools/count/main.nf
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* raxml-ng is compute intensive - upgrade process label to high
* ensure raxmlng uses --all when bootstrapping
* remove block that should be taken of by the options passed in
* update tests
* Bump version and format references to use raw params.test_data
* Apply suggestions from code review
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Updated tags
Missed on in last commit.
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Add new human data and fix sarscov paths
* Fix filename typo
* Apply code review
* replace index with to match sarscov data
* lower case
* indent everythin
* Adapt sarscov keys to new naming convention
* Update test_data.config
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update HISAT2 build module
* Bump preseq version
* Fix tests
* Add meta.yml for preseq to fix linting
* Auto-detect --genomeSAindexNbases for smaller genomes
* Add placeholder to use human data for the tests
* Add CSI output option to samtools/index
* Fix samtools/index tests
* new raxml module
* new raxml module
* pass in args for bootstrap and add test for support file
* remove unnecessary tag
* ensure tags meet guidleines
* Apply suggestions from code review
* Update to latest functions file
Co-authored-by: avantonder <avt@sanger.ac.uk>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Adding bigWig and deeptools computeMatrix files to config
* Adding meta.yml for deeptools modules
* Add test for deeptools modules
* Fixing and reordering tags
* Fixing conda test that worked in local...
* Apply suggestions from code review
* Changing bigwig file pattern to include bigwig extension
* Saving after last change is a good practice
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Resolve suggests after PR review
* add newline to functions
* need variable interpolation using double quotes; remove unnecessary tag
* add a more resilient link to raw github files
* remove trailing slash
* Update software/iqtree/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
