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Created with Raphaël 2.2.027Jan21201521Dec829Jul12Jun8522Apr31Mar25231325Nov4Oct11Sep28Aug272623222119142Jul126Jun24191176324May1615225Apr121142128Mar1815145422Feb2019151331Dec30Oct29242317411Sep26Jul1214Jun17Apr26Mar22161413Add scriptssingularity_devsingularity_devAdd conda dependenciesCreate directory for docker imagesAdd dockerfilesingularitysingularityEdit snakefile java commands to work with conda installed softwareAdd first environment.yml for condaSnakemake : (re) add rulesmastermasterMerge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into developdevelopdevelopvcf_filter_annot : deal with empty fileMerge branch 'develop'change author affiliationmerge developupdate READMEupdate READMEadd imagechange string encoding in variantFiltrationadd phaser_expr_matrixSnakemake 1000RNASeq_chicken/calling : update STAR Aln memory resourceMerge branch 'develop'Snakemake RNAseqVariantCalling: finalization of RNAseqVariantCalling pipeline1000RNASeq calling: change partition attribut name in resources_SLURM.yamlRNASeqVariantCalling : rename SnakefileSnakemake RNSAseqVariantCalling : update documentation workflow and clean up1000RNASeq_chicken/ASE : finalize snakemake pipelineResolve conflict before mergingSnakemake 1000RNASeq chicken/ase : add developpment status in the README fileSnakemake 1000RNASeq chicken/ase : change variant filtering procedure and update ressourcesSnakemake 1000RNASeq chicken/calling : update SLURM.shSnakemake 1000RNASeq ASE : debug vcf_annotator, change script in execution mode, correct VCF_for_ASE_and_table ruleSnakemake 1000RNASeq ASE : add summary script for trimgalore, star and to convert phred scaleSnakemake 1000RNASeq ASE : add script dir in PATHSnakemake 1000RNASeq ASE : add bedtools dependency in config.yamlMerge branch 'develop' of forgemia.inra.fr:bios3biol/workflows into developSnakemake 1000RNASeq ASE: correct GATK4 VariantFiltration filter syntaxeSnakemake 1000RNASeq ASE: add quality trimming threshold in Trimgalore rulesSnakemake 1000RNASeq ASE: correct script syntax in gtf2bed ruleSnakemake RNAseqVariantCalling : report 1000RRNASeq_chicken/calling update: quality trimming and trimgalore_summaryMerge branch 'develop' of forgemia.inra.fr:bios4biol/workflows into developSnakemake 1000RNASeq : add fastq quality filtering threshol at 15 by default1000RNASeq calling : bug fix in script/trimgalore_summary.py when sample are all single end sequenced