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Verified Commit 3970e25b authored by Laurent Modolo's avatar Laurent Modolo
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add script to run benchmark

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# 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
#
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