* 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
* modified yml to allow new subworkflow testing
* Update test.yml
* Update test.yml
* updated to follow the new mergebam syntax, also made unaligned input sample specific
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
* refactor: add bcl2fastq to cellranger dockerfile
bcl2fastq required for the cellranger mkfastq module and was therefore
added to the cellranger dockerfile. Further, cellranger was updated to
the latest version, 6.1.2., with naming and containers across
cellranger modules updated accordingly.
* chore: add bcl2fastq zip to .gitignore
* style: fix code linting error
* test(cellranger): Add tiles to mkfastq
* additional dockerfile for mkfastq
* update readme and dockerfiles
* update readme
* fix: update container for mkfastq
* docs: correct typos in readme
* test: update md5sum following cellranger update
* test: update md5sum following cellranger update
* fix: new line for external args in mkfastq
* test: update mkfastq tiles argument
* test: comment out mkfastq tests until smaller test data found
* test: stub-run mkfastq test until smaller test data found
* test: fix incorrect file path for mkfastq
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: ggabernet <gisela.gabernet@qbic.uni-tuebingen.de>
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
* Bump version 0.1.5 to chromap/chromap
* Bump conda samtools version to 1.14
* Get read of inconsistent md5sum in conda
* Bump version in conda and retry md5 checks
* genome index md5 hash removed, conda failed
* Remove old nextclade module
* Add nextclade/datasetget and nextclade/run modules
* Fix ECLint
* Add reference and tag as inputs to datasetget module
* Fix tests
* Adjust spacing
* Add stubs for deepvariant [ci skip]
* Update the stubs for deepvariant [ci skip]
* functional with google docker image
* cleanup
* consume docker container within singularity executor
* update the meta.yml file and ask for review
* tweak the input channel shape and test data
* tweak input data [ci skip]
* update for the new syntax
* remove the functions and rename meta vars
* Update the arguments mechanism
* update chr, region and checksum
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* Update dsh-bio to version 2.0.7, add support for compressed GFA 1.0 format
* fix ci failures
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
* Add functionality to handle vbz compression
In order for nanopolish to be able handle the default compression for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution
* Make the HDF5_PLUGIN_PATH more configurable
Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g
```
params {
modules {
.....
'nanopore_artic_minion' {
.....
hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
}
......
}
}
```
* Update modules/artic/minion/main.nf
* Export HDF5_PLUGIN_PATH
The HDF5_PLUGIN_PATH variable should be exported for `artic minion` to use it
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update seqwish to version 0.7.2
* seqwish can work with a comma-separated list of PAFs
* level with nf-core/modules master branch
* add pangenome test data keys
* the odgi test data lives in its own folder
Co-authored-by: Michael L Heuer <heuermh@acm.org>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
* Add functionality to handle vbz compression
In order for nanopolish to be able handle the default compression for Mk1C Minions (vbz) it must be aware of where to find the plugin. Exporting the HDF5_PLUGIN_PATH found in the conda install (also used to make the biocontainer image) is the solution
* Make the HDF5_PLUGIN_PATH more configurable
Allow the HDF5_PLUGIN_PATH to be changed via a section in a config file e.g
```
params {
modules {
.....
'nanopore_artic_minion' {
.....
hd5_plugin_path = '/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin'
}
......
}
}
```
* Update modules/artic/minion/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Bump software versions for viralrecon modules
* Remove custom params.save_unaligned from bowtie2_align
* Unify samtools modules and error if input and output names are the same
* Fix ALL the tests
* Removed if-statement to only run on more than 1 file, now it will run on single files as well.
* Added a test for running the cat_cat module on a single file.
* Created a new test.yml with nf-core modules create-test-yml -t cat/cat
* Edited test.yml to not include paths and md5sums for versions.yml, and also removed sometimes variable md5sums
* Added files for bcftools/sort
* Fixed output format and removed md5 checksum
* Change input to avoid identical in/output names
* Created rows for bcftools/sort in pytest_modules.yml
