update to be in-line with ESR #2
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Awesome update allowing easy cohort analysis.
Allow user to set the adapter trimming settings
Fix multiqc wrapper + slurm issue
Merge cpu and gpu pipelines
Add optional fastq trimming
Integrate trimming reports into multiqc report
Allow per rule/sample resource configuration + other fixes
As it stands, this causes an error at gatk_GenotypeGVCFs for cohort runs
* 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
* 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)
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