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Xavier Grand
ChIPster
Graph
9e61e551a817ca609d3b24217014a396238a2c76
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master
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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
gatk4: change Xmx option parsing
nf_modules: add gatk4
nextflow.config: remove space in memory declaration
macs2: caputre *_peaks.xls for multiqc report
bwa: add quote surrounding -R option
bwa: fix bwa_mem_R call
bwa: add params.bwa_mem_R variable
picard: fix output name of index_fasta
picard: main.nf: improve output index_fasta output
picard: improve picard index output
samtools: fix merge_multi_bam
samtools: fix merge_multi_bam
macs2: add file_id to output
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