* fix: remove left-over unnecessary code
* Add prinseq++
* Remove last todo
* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)
* Apply suggestions from code review
* callcnvs stub and tests
* partition stub and test
* histogram stub and test
* importreaddepth stub and tests
* update module scripts
Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
* 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
* add meta to samtools/faidx
* move to bgzip
* update freebayes test results
* bump pydamage version to 0.70
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>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* fix(homer): Update tagdir to have a prefix
Otherwise they have a naming collision
* test(homer): Update paths
* style(homer): Align ,'s
* chore(homer): Update md5sums
* controlfreec significance
* move freec files to own subfolder
* Fix meta.yml naming
* Fix meta.yml naming
* Fix linting
* Forgot to refactor
* forgot more refactoring
* Too much refactoring on output paths
* Too little refactoring here
* update checksum
* Use meta map and supply output file name via modules.config
* Remove all def declarations to make it work
* update tests & remove extra .
* fix ze tests
* update meta.yml with meta map info
* add tag line now that meta is available
* Mpileup also likes intervals
* Also update meta yml with inclusive input and intervals
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
* fix(homer): Update expected file path to improve caching
* docs(homer): Update findpeaks
* test(homer): Add maketagdirectory dependency
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* feat(bbmap): Initialize pileup module
* test(bbmap): Update outputs
* test(bbmap): Add pileup tags
* style(bbmap): Add in when
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* feat: add template for Bracken
* chore: update version
* refactor: change command build
* refactor: rename report variable, change quotes
* docs: remove refactored input parameter
* fix: correctly assign arguments to options
* tests: set up single and paired end tests
* style: apply prettier
* chore: change data sources to official ones
* refactor: rename test workflows
* tests: use correct input to the new UNTAR module
* chore: update md5sums
* fix: remove left-over unnecessary code
* Adds support for meta lists for unzip and untar
* Fix test inputs
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Fix MALTEXTRACT/AMPS
* Fix further modules
* Fix cellranger
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* fix: remove left-over unnecessary code
* Switch to more portable solution for singularity container issue by using bind paths
* Fix input collision of dummy files
* Repalce dummy with which bash
* Remove dummy usage from tests
* Apply suggestions from code review
* Fix singularity typo
* style: Add prettier config files
* build: Add prettier vscode extension
* ci: Replace markdownlint and yamllint with prettier
* style: Run prettier
* style: Use indent of 2 for markdown as well
https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358
* style: Fix indent
* style: Let editorconfig take over tab widths
* style: yaml => yml
* ci: Run prettier once
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
* fix: remove left-over unnecessary code
* Adds --fakeroot option for singularity usage with DeepARG as workaround for broken conda dependency
* Update modules/deeparg/downloaddata/main.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Update modules/deeparg/predict/main.nf
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Apply suggestions from code review
* Update main.nf
* Update main.nf
* Update main.nf
* Update main.nf
* Go back to original logic
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* First commit
* putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it
* adding first try of relevant commands (not working yet, just took their basic pipeline example
* test commit
* remove test
* starting up work with module after 3.0.0 upgrade
* add ascat.prepareHTS statemet
* add location of docker for new mulled alleleCounter+ASCAT container
* first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
* add notes on dropbox download
* use a newer pytest_modules.yml
* add outpit
* trying to align with current Sarek output
* adding in FH comments
* busy clearing up arguments and testing. Still WIP
* first working run, in nextflow, with sarek-like output. Still needs more work on input arguments
* cleaning up before writing up findings
* testing with putting in arguments in args
* draft for solution 3 style for arguments
* one more test added
* adding FH map
* finished testing maps for args
* wrap-up cram/crai test successfully
* updates to address ability to put in ref.fasta argument for cram running
* adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config
* first test with auto-downloading the s3-data (when not given as an argument)
* removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug
* adding mulled singularity container
* removing tests
* fix left padding lint issue
* lint failure in meta.yml
* more linting errors
* add when argument
* adding stub functionality
* add stub run
* correct md5sum for versions.yml
* more testing with -runstub
* stub code in pure bash - not mixed with R
* reformat version.yml
* get rid of absolute paths in test.yml
* correct wrong md5sum
* adding allelecount conda link
* rename normal_bam to input_bam etc
* let the pipeline dev worry about matching the right loci and allele files
* dont hardcode default genomebuild
* adding download instruction comment
* add doi
* fix conda addition bug
* add args documentation
* test new indent
* new test with meta.yml indentation
* retry with new meta.yml
* retry with new meta.yml - now with empty lines around
* retry with new meta.yml - remove trailing whitepsace
* trying to fix found quote character that cannot start any token error
* try with one empty line above triple-quote and no empty line below
* trying with pipe character
* checking if its the ending triple quote
* one more try with meta.yml
* test update bioconda versioning for linting failure
* test update bioconda versioning for linting failure 2
* testing allelecounter version error on conda
Co-authored-by: @lassefolkersen
Co-authored-by: @FriederikeHanssen
