Kevin Menden
f7e3b8260c
change process.time for tests to 2h ( #452 )
2021-04-16 13:08:03 +01:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests ( #365 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
* Initial commit for test data config
* Rename test data
* Include test config
* Update indents
* Update test for FastQC via config
* Remove quotes of bottom-level variables
* Use underscores in key names
* Get tests working for fastp
* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module ( #173 )
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* Normal bam file added
* Normal bam.bai file added
* Tumour bam bai files added
* human dir added
* annotation dir added
* cnvkit dir added
* cnvkit dir added
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* changed input filenames
* edited main.nf
* edited main.nf
* edited meta.nf
* edited test.yml
* filters.yml
* edited main
* edited main
* edited meta
* edited meta
* edited main
* removed unwanted lines
* edited the path to the main.nf
* removed function.nf
* added functions.nf
* deleted 2 workflows and craeted a common workflow
* deleted paths for 2 workflows and created paths for a common workflow
* Deleted annotation dir
* deleted params.modules
* Edited meta.with_normal
* deleted normal_280_sub_chr21.bam
* deleted normal_280_sub_chr21.bam.bai
* deleted tumour_278_sub_chr21.bam
* deleted tumour_278_sub_chr21.bam.bai
* Edited input and script parts
* Edited input part
* Added
* Edited args
* Edited script
* Edited input
* Changed annotation to annotationfile
* Changed description of the tool
* edited singularuty container
* edited input
* line 44 removed trailing whitespace
* Edited addParams
* Deleted pdf output
* Deleted pdf output
* edited the path to main.nf
* edited path to the main.nf
* Added docker image version
* Removed extra ../
* added md5sums
* added md5sums
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Edited the script
* Edited the input
* Edited main.nf
* Edited main.nf
* edited md5sum for reference.cnn
* removed human fasta
* removed human fasta.fai
* added GRCh38 fasta
* added GRCh38 fasta.fai
* added hg19 fasta.fai
* added hg19 fasta
* Edited fasta file name
* Edited bed file names and md5sums
* Edited md5sums
* edited the input and script section
* edited input section
* added targetfile
* changed the files
* changed the output files
* added bam files
* added bam files
* remove files
* added md5sums
* replace file
* added files
* edited tests/software/cnvkit files
* edited tests/software/cnvkit files
* edited authors list
* removed files
* added files
* added files
* added files
* added files
* added file
* added file
* added file
* added file
* edited files
* edited files
* edited files
* edited files
* edited files
* edited files
* added new module
* added new module
* edited files
* edited file
* edited file
* edited file
* removed files
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Harshil Patel
d1cb9a845f
Check for minimum NF version ( #278 )
2021-03-18 12:00:32 +01:00
MaxUlysse
4968458b6c
chores: add cpus, memory and time requirements to limit resource consumption
2021-02-16 14:18:29 +01:00
drpatelh
fe3cb87f6d
Direct download Singularity containers
2021-02-03 20:03:45 -06:00
Edmund Miller
467d1595c4
test: Use docker image with singularity
2021-02-02 18:14:39 -06:00
Edmund Miller
72b4fb35aa
test: Fix profile logic order
2021-02-02 17:32:21 -06:00
Edmund Miller
67deb0d47a
ci: Add singularity tmp dir
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:25:58 -06:00
Edmund Miller
6b675eef6d
ci: Set pull docker container to false
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-02-02 17:00:40 -06:00
Edmund Miller
ddbca7b467
test: Use profile ENV variable hack
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The user will now set the env variable and pass it to pytest. You also
can't set the env variable ahead of time, it has to be run with pytest.
Example:
PROFILE=conda pytest --tag fastqc --symlink --kwd
2021-02-02 12:44:30 -06:00
Edmund Miller
b96f2d6a5e
test(config): One config to rule them all
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2020-11-24 20:26:04 +00:00
