From 3970e25b7c9bd2c4fd6e8f55dfbe9f4c8d258417 Mon Sep 17 00:00:00 2001 From: Laurent Modolo <laurent.modolo@ens-lyon.fr> Date: Thu, 25 Jul 2024 10:25:28 +0200 Subject: [PATCH] add script to run benchmark --- script_parasplit_local.sh | 246 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 246 insertions(+) create mode 100644 script_parasplit_local.sh diff --git a/script_parasplit_local.sh b/script_parasplit_local.sh new file mode 100644 index 0000000..913a783 --- /dev/null +++ b/script_parasplit_local.sh @@ -0,0 +1,246 @@ +# cutsite + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_cutsite_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --save_bam \ + --cutsite \ + -with-report \ + -resume --max_memory 60GB + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_cutsite_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --cutsite \ +# -with-report \ +# -resume --max_memory 60GB +# +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_cutsite_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --cutsite \ +# -with-report \ +# -resume --max_memory 60GB + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_cutsiteseed0_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --save_bam \ + --cutsite --cutsite_seed 0 \ + -with-report \ + -resume --max_memory 60GB + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_cutsiteseed0_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --cutsite --cutsite_seed 0 \ +# -with-report \ +# -resume --max_memory 60GB +# +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_cutsiteseed0_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --cutsite --cutsite_seed 0 \ +# -with-report \ +# -resume --max_memory 60GB + +# parasplit + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_parasplit_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --parasplit \ + -with-report \ + -resume --max_memory 60GB + + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplit_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --parasplit \ +# -with-report \ +# -resume --max_memory 60GB +# +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplit_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --parasplit \ +# -with-report \ +# -resume --max_memory 60GB + + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_parasplitseed0_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --parasplit --parasplit_seed 0\ + -with-report \ + -resume --max_memory 60GB + + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitseed0_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --parasplit --parasplit_seed 0\ +# -with-report \ +# -resume --max_memory 60GB +# +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitseed0_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --parasplit --parasplit_seed 0\ +# -with-report \ +# -resume --max_memory 60GB +# +# ############################## +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitfr_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --parasplit --parasplit_mode "fr" \ +# -with-report \ +# -resume --max_memory 60GB + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_parasplitfr_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --parasplit --parasplit_mode "fr" \ + -with-report \ + -resume --max_memory 60GB + + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitfr_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --parasplit --parasplit_mode "fr" \ +# -with-report \ +# -resume --max_memory 60GB +# +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitfrseed0_filter_pcr \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_pcr \ +# --parasplit --parasplit_mode "fr" --parasplit_seed 0\ +# -with-report \ +# -resume --max_memory 60GB + +./nextflow run main.nf \ + -profile docker \ + --workflow hicstuff \ + --input data/samplesheet.csv \ + --fasta data/S288c_DSB_chr3_rDNA.fa \ + --outdir results/hicstuff_parasplitfrseed0_nofilter \ + --digestion arima \ + --bin_size '1000' \ + --save_bam \ + --parasplit --parasplit_mode "fr" --parasplit_seed 0 \ + -with-report \ + -resume --max_memory 60GB + + +# ./nextflow run main.nf \ +# -profile docker \ +# --workflow hicstuff \ +# --input data/samplesheet.csv \ +# --fasta data/S288c_DSB_chr3_rDNA.fa \ +# --outdir results/hicstuff_parasplitfrseed0_filter \ +# --digestion arima \ +# --bin_size '1000' \ +# --filter_event \ +# --parasplit --parasplit_mode "fr" --parasplit_seed 0\ +# -with-report \ +# -resume --max_memory 60GB +# -- GitLab