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Xavier Grand
ChIPster
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9f50974db7a86cfbbf92d59166c520f2a0f942d2
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gatk4: change output to avoid using file_id var as it can be a dict
minimap2: add main.nf
Docker: add minimap2:2.17
g2gtools: add convert process
bwa: add single_end mapping
add missing pairend_end & single_end switch
add paired_end and single_end switch version to all implementations
fastp: test paired_end & single_end process
bwa: fix file_id definition
bwa: fix bug :46
bwa: fix previous commit
bwa: conditional definition of the library tag
bwa: fix bam tag format
Docker: add star 2.5.3
gatk4: make gvcf_genotyping emit vcf.gz files
Docker: g2gtools, add procps for nextflow
Docker: fix g2gtools dependencies
.gitignore: ingore vscode file
g2gtools: add incorporate_snp and incorporate_indel processes
Docker: g2gtools add pysam dependency
g2gtools: add vci_build process
gatk4: fix option for Haplotypecaller
gatk4: change recalibrate_snp to pair recall_table with BAM
gatk4: switch PrintRead to ApplyBQSR
gatk4: add vcf indexing for BaseRecalibartor
gatk4: fix BaseRecalibrator params
gatk4: fix VariantFiltration params
gatk4: update SelectVariants options
gatk4: fix SelectVariants cmd (remove -T)
gatk4: remove spark...
gatk4: fix java-options
gatk4: change -o to -O
gatk4: fix spark config
gatk4: change -nct to --spark-master option
gatk4: remove unnecessary -T option
gatk4: try to fix task memory parsing
gatk4: add G unit to xmx params
gatk4: add xmx_memory parsing for every process
docker: add r 4.0.3
gatk4: fix typo :264
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