Release v2.1.0 (#24)

* Add rule and sample info to slurm log files

* Get naming convention of log output dir consistant

* Add pipeline tests (#14)

* Add test dataset

* Add info on test dataset

* Automate setting up to run test dataset

* Speedups (#15)

* Use full parabricks germline pipeline + other standalone tools - provides speedups

* Thread parabricks rules

* Remove snakemake wrapper and thread fastqc

* Add fastqc conda env now that snakemake wrapper has been removed

* Fixes

* fix error due to file target that isn't created

* forgot to add parabricks rule to local rule list

* remove flag that causes error

* allow dynamic inclusion of recal resources - also stop need for user … (#17)

* allow dynamic inclusion of recal resources - also stop need for user to manually write the flags

* clarify you can directly pass adapters to trim galore

* move existing helpers functions to one place in snakefile

* simplify flags for WES settings

* account for when someone doesn't use WES settings

* Simplify code (#19)

* Functionize code (#20)

Move dynamic stuff (like if-else statements) into functions to avoid having global variables

* Docs (#22)

* separate docs for running in different situations

* add images

* fix links to images

* add section about getting data on nesi

* remove incomplete docs for running pipeline on NeSi for now

* fix fastqc/multiqc error

* improve documentation

* fix file path that makes download from google cloud bucket not work

* improve docs

* discourage using home dir in docs

* add more information about pipeline

* fix sample wildcard error for rules without sample wildcard

* clarify output files

* add link to discussions

* remove g.vcf that causes error in vcf_annotation_pipeline (#25)

Dev (#23)

* Add rule and sample info to slurm log files

* Get naming convention of log output dir consistant

* Add pipeline tests (#14)

* Add test dataset

* Add info on test dataset

* Automate setting up to run test dataset

* Speedups (#15)

* Use full parabricks germline pipeline + other standalone tools - provides speedups

* Use full parabricks germline pipeline + other standalone tools - provides speedups

* Thread parabricks rules

* Remove snakemake wrapper and thread fastqc

* Add fastqc conda env now that snakemake wrapper has been removed

* Fixes

* fix error due to file target that isn't created

* forgot to add parabricks rule to local rule list

* remove flag that causes error

* allow dynamic inclusion of recal resources - also stop need for user … (#17)

* allow dynamic inclusion of recal resources - also stop need for user to manually write the flags

* clarify you can directly pass adapters to trim galore

* move existing helpers functions to one place in snakefile

* simplify flags for WES settings

* account for when someone doesn't use WES settings

* Simplify code (#19)

* Functionize code (#20)

Move dynamic stuff (like if-else statements) into functions to avoid having global variables

* Docs (#22)

* tweaks to docs

* seperate docs for running in different situtations

* minor

* add more info on how to contribute

* fix links

* fix typo

* sounds less desperate haha

* fix link to doc

* update

* add images

* fix links to images

* fix links to images

* update

* add section about getting data on nesi

* remove incomplete docs for running pipeline on NeSi for now

* fix fastqc/multiqc error

* improve documentation

* improve documentation

* fix file path that makes donwload from google cloud bucket not work

* improve docs

* discourage using home dir in docs

* improve docs

* improve docs

* improve docs

* add more information about pipeline

* minor

* improve docs

* fix sample wildcard error for rules without sample wildcard

* clarify output files

* improve docs

Patch_1 (#13)

* Patch_1

* Revert Readme

* Revert readme

Make gatk conda env compatible with parabricks gatk version

As it stands, this causes an error at gatk_GenotypeGVCFs for cohort runs