Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/hub/hic

script_parasplit_local.sh

+# 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
+#