* New last/lastal to align query sequences on a target index
`lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last)
suite. It align query DNA sequences in FASTA or FASTQ format to a
target index of DNA or protein sequences. The index is produced by
the `lastdb` program (module `last/lastdb`). The score matrix for
evaluating the alignment can be chosen among preset ones or computed
iteratively by the `last-train` program (module `last/train`). For
this reason, the `last/lastal` module proposed here has one input
channel containing an optional file, that has to be dummy when not used.
The LAST aligner outputs MAF files that can be very large (up to
hundreds of gigabytes), therefore this module unconditionally compresses
its output with gzip.
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).
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Un-hardcode the path to the LAST index.
Among multiple alternatives I have chosen the following command to
detect the sample name of the index, because it fails in situations
where there is no index files in the index folder, and in situations
were there are two indexes files in the folder. Not failing would
result in feeding garbage information in the INDEX_NAME variable.
basename \$(ls $index/*.bck) .bck
In case of missing file, a clear error message is given by `ls`. In
case of more than one file, the error message of `basename` is more
cryptic, unfortunately. (`basename: extra operand ‘.bck’`)
Alternatives that do not fail if there is no .bck file:
basename $index/*bck .bck
find $index -name '*bck' | sed 's/.bck//'
Alternatives that do not fail if there are more than one .bck file:
basename -s .bck $index/*bck
ls $index/*.bck | xargs basename -s .bck
find $index -name '*bck' | sed 's/.bck//'
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* New last/split module to find split alignments.
The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last)
finds split or spliced alignments in a MAF file that is produced with, for
example, LAST `lastal` command.
This new module is part of the work discribed in Issue #464. During this
development, we fix the versiob of LAST to 1219 to ensure consistency. We will
upgrade it later.
* Update software/last/split/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* add additional ucsc tools
* Update software/ucsc/wigtobigwig/meta.yml
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed.
Co-authored-by: Kevin Menden <kevin.menden@live.com>
* 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>
* 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>
* 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>
* 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>
* 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>
* 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>
* Add abacas module
* Add test for abacas module
* Add Harshil to authorship
* Updating test with the data uploaded to nf-core/datasets
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
* fixing a bunch of module tests
* remove vscode
* fixed minia
* move test data directory to nf-core/test-datasets
* bump multiqc version
* remove the test data
* updated test data link
* update README
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new submodule mash/sketch
* fixed submodule naming
* OK, tag is diff to keyword
* OK another round 🤣
* removed TODO comments
* updated as per review comments 🙆♂️
* updated functions.nf 😁
* Update software/mash/sketch/main.nf
* Update main.nf
Removed blank line at the 12th
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* new module: rasusa
* Removed blank line in software/rasusa/main
* updated code as per reviewcomments
* removed blank line as failed for lint
* updated as per review comments
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me
* Removed trailing whitespace line 29
* Moved workflow from meta to options.
* Update main.nf
* Forgot to remove previous testing input channel for workflow.
* Apply suggestions from code review
Applied changes suggested by @drpatelh
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Added gtf to meta.yml.
* Apply suggestions from code review
Adding @drpatelh suggested changes.
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Moved workflow to input value. Fixed tests.
* Update tests/software/kallistobustools/ref/test.yml
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
