Outsourced all settings to config.env#4
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* New syntax for picardFold According to warning message and https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) * Added software sources * Create A0b_MasterListFiltering.m * Update 2_CombiScriptSamtools.sh samtools does not support mpileup -> use bcftools * Update 2_CombiScriptSamtools.sh * Update 2_CombiScriptSamtools.sh * Update 2_CombiScriptSamtools.sh * new folder called dictionary * Update README.md * Update README.md * add dictionary files * add dictionary files * Update README.md * change folder name * Update A2_Lists2Genes.m * Add the Insertion script * Update 3_CombiScript_Insertions.sh * Update 3_CombiScript_Insertions.sh * Update README.md * Add files via upload * Update and rename A7_Cov2Ins.m to A4_Cov2Ins.m * Add files via upload * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Add files via upload * Add files via upload * Delete Pipeline_WGS.png * Add files via upload * Delete Pipeline_WGS.png * Add files via upload * Delete Pipeline_WGS.png * Add files via upload * Update README.md * Add files via upload * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Delete Pipeline_WGS.png * Add files via upload * Update README.md * Update README.md * Delete CM_Pipeline_WGS.png * Add files via upload * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Create README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Add files via upload * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Update README.md * Add toy data to repository * .. * Delete Wns1720.5_bcfcall.vcf * Delete Wns1720.5_2NCe_coverage.txt * Update README.md * Update README.md * Update README.md * Update README.md * Update A0_VariantFiltering.m * Update A1_SNP2CNP.m * Update A1_SNP2CNP.m * Update A2_Lists2Genes.m * Update A2_Lists2Genes.m * Update A1_SNP2CNP.m * Update A0_VariantFiltering.m * Delete Wns1720.zip * update * Delete Wns1720_5_coverage.txt * update * Update A1_SNP2CNP.m * Update A2_Lists2Genes.m * Update A2_Lists2Genes.m * Update A2_Lists2Genes.m * Add files via upload * Add files via upload * Add files via upload * Update A2_Lists2Genes.m * Update A3_Cov2DelDup.m * Update A3_Cov2DelDup.m * Update A4_Cov2Ins.m * Update README.md * Update README.md * Update README.md * Update README.md --------- Co-authored-by: Easybel <57913876+Easybel@users.noreply.github.com> Co-authored-by: Easybel <irathman@uni-koeln.de>
With this version, settings like paths, threads, RAM etc. are moved to config.env which is imported by the actual scripts. Other changes: - added RAM parameter to samFold - removed 20 in grep in 3_CombiScript-Insertions.sh
Remove doubled declarations
Small tool to filter rows of struct in a .mat file by given criteria and save to new .mat. Useful to acquire e.g. AccMM2Genes.mat.
Fix wording
donr --> donor
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With this version, settings like paths, threads, RAM etc. are moved to config.env which is imported by the actual scripts.
Other changes:
Perhaps there are bugs with the automatic file names for $i since I did not test it with SLURM.