Final bug fixes before submitting the paper#7

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MaartenPostuma wants to merge 318 commits intoepiGBS2v2from master

+3,022-1,841

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Commits on Jan 20, 2021

Reference hack doesn't seem to be necessary!
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Add merge step
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Snakemake syntax??
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Typo
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Typo
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Removed field that stopped merging from being possible
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Added filter for sites with no alt allele and for which the reference allele = N
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Added reference branch
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Added reference branch (SNP_calling does not work yet)
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Update reference.rules
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Update reference.rules
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test
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should work now
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Should actually work now
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typo
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Commits on Jan 21, 2021

Commits on Jan 22, 2021

Simplified snakemake structure
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Missed commas
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Dictionary was in the wrong place
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Updated config. Renamed legacy to legacy
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Re-added QC
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Commits on Jan 25, 2021

Changed rule multiQC to work with new pipeline
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Update Snakefile
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Missing comma
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Forgot rules/
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Added Fleurs environments + removed removed old reference branch
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Added output to demultiplex.rules so it works with the new version
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Removed duplicate lines from demultiplex.rules as they should be in the Snakefile
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Synthaaaaaaaaaax
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Update demultiplex.rules
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Commits on Jan 26, 2021

Removed unused rules files
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Attempted fix not all tmp files deleted. Adjusted default denovo parameters
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Maybe do not delete these files?
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Commits on Jan 27, 2021

Removed QC from legacy branch (temporary?)
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Update Snakefile
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Update Snakefile
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Commits on Jan 29, 2021

Added sexy new multiqc
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Fixed parse log input
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???
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?!
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????
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Fixed outdir
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added QC to the legacy branch
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Commits on Feb 1, 2021

Fixed temp files not being deleted
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?
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New attempt for proper temp file management
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More temp file changes
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Reference branch should work the same as the denovo branch... Denovo branch should work
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Syntax
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Fixed variable names not correct
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Slightly better tmpdir structure for demultiplexing
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Commits on Feb 2, 2021

removed SNP calling parameters from the legacy branch
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Commits on Feb 3, 2021

typo
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Changed rule all so you don't create the watson/crick files that you do not use
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typo
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Update fastqc-ref.rules
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Renamed rules to reference instead of denovo
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Commits on Feb 4, 2021

New improved snp_calling?
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Update ProperSNPCallingReference.rules
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Commits on Feb 5, 2021

Added improved SNP calling + moved multqc creation to before SNP calling case you want to skip it
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Synthax
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Correct environment location
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Commas and removed un used script
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Incorrect environment path
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Commits on Feb 11, 2021

Fixed dictionary not being created correctly when . are present in genome name
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Update README.md
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Update README.md
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Commits on Feb 15, 2021

Minor update to when fastqc is started
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Commits on Feb 22, 2021

Branch Test
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Non-directional mapping
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Attempt to get trimming to wrok
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To many brackets
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Removed part that I now skip
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Fixed synthax error
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All rules get their own name
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Added adams python script
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Commits on Feb 23, 2021

Create benchmarking.txt
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Added better SNP calling to reference branch
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Forgot comma
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Out_dir != output_dir
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Snakemake synthax many files in few files out is complex
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Conda environment names
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Added new SNP calling to denovo branch
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The denovo branch does not have a reference before you run it...
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Update denovo.rules
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Update denovo.rules
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Better threads usage + config update + denovo creation parameters change
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Commits on Feb 24, 2021

Changed calmd to run on the big file
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Update reference.rules
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Update reference.rules
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Fixed multiQC not working as intended
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Added multicoreness to samtool commands were ncessariy
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Input != output
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Added index after calmd
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Fixed missing comma's
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Added index + removed uncessary temp() input lines in trimming
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Learn to spel parralel
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Index prepared bam
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make tmp paths make sense
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Update reference.rules
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More paths
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Added RG properly in the bam files
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No more cut adapt logs in the rule all
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Typo
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location of mutliqc config file
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Update fastqc-ref.rules
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Give the correct things the correct name and not the incorrect things an incorrect name
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Commits on Feb 25, 2021

No multicore for denovo branch
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Update to ensure samtools merge doesn't output 10.000 header lines
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Denovo can ben multithread again!
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Now fastqc always works
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Added -Q parameter to ensure Qualities are masked
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Commits on Mar 2, 2021

Adding mapping quality to snp calling
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Update fastqc-ref.rules
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Update fastqc-ref.rules
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Commits on Mar 3, 2021

(hopefully) changed module order in multiQC
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Commits on Mar 4, 2021

added "running multiple lanes"
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Update reference.rules
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updated Read me
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Merge branch 'SneakyImplementationOfAdamsSNPcaller' of https://gitlab.bioinf.nioo.knaw.nl/MaartenP1/epigbs2 into SneakyImplementationOfAdamsSNPcaller
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Correct qualities in SNP calling
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added --no-population-priors
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Commits on Mar 10, 2021

Update reference.rules
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Update fastqc-ref.rules
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Commits on Mar 16, 2021

Update denovo.rules
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Commits on Mar 18, 2021

Added trimmed fastqc?
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Typo
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Commits on Mar 22, 2021

Cleaning
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typo
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Typo's
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Update README.md
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Added parameters of SNP calling to rules files
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Merge branch 'SneakyImplementationOfAdamsSNPcaller' of https://gitlab.bioinf.nioo.knaw.nl/MaartenP1/epigbs2 into SneakyImplementationOfAdamsSNPcaller
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Commits on Mar 24, 2021

add exception in parsing script to allow reference branch.
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Commits on Mar 30, 2021

Commits on Apr 12, 2021

Added parameterTest Things
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update Snakefile
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Update Snakefile
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Update Snakefile
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Update Snakefile
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Update Snakefile
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Update paramTest.rules
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Jaaaaaaaaaa hooooooooor
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Commits on Apr 13, 2021

Fixed temp file issues + clustering ID incorrect values
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TAB seperated file
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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This works
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test
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Update paramTest.rules
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Fixed the issue!!
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???!!!
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Commits on Apr 14, 2021

Fixed the issues with the tmp files
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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New idea
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hahahaha
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Update paramTest.rules
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Commits on Apr 19, 2021

added stacks logs to multiqc in reference branch
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added mulitqc stacks support
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Update README.md
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Commits on Apr 20, 2021

Making datasets for plots
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Update paramTest.rules
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Added plot script, cleaned up the file structure
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Update paramTestPlot.R
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Update paramTestPlot.R
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Merge branch 'SneakyImplementationOfAdamsSNPcaller' of https://gitlab.bioinf.nioo.knaw.nl/MaartenP1/epigbs2
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Typo
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Commits on Apr 22, 2021

Typo
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Update multiqc.yaml
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Stop annoying warning message from appearing
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Commits on Apr 30, 2021

Add .gitlab-ci.yml to test quality of the code
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Merge branch 'SneakyImplementationOfAdamsSNPcaller' into 'master'
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Commits on May 5, 2021

Update README.md
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Merge branch 'master' into 'master'
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Commits on Jun 9, 2021

Update reference.rules
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Commits on Jun 11, 2021

Removed incorrect information in comment
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Removed incorrect information from comment
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Commits on Jun 16, 2021

Update bismark.yaml so it does work on the NIOO server! (And probably some other servers in the world aswell)
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Commits on Jul 20, 2021

Better default parameters for parameter_test
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Fixed bugs in paramTest.rules that caused the removal of temp files which were in use + fixed data.frame not being populated properly
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Commits on Oct 12, 2021

Commits on Nov 3, 2021

Improved performance of clone_filter by using a newer version of stacks
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Commits on Jan 19, 2022

Added polyG problem and clone_filter memory issues to the error section of the readme
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Commits on Jan 20, 2022

Commits on Jan 25, 2022

added some minor changes
FleurGaBru
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