Primary tool used in this pipeline - https://github.com/tf2/CNest
This pipeline can run in two modes -
- Running End to end for all the steps
- Running individual steps
nextflow run main.nf \
--project "1kgp_subset_test" \
--design "testdata/1kg_CEU_7_samples_subset.csv" \
--bedgz "testdata/hg38.1kb.chr-19-22.baits.bed.gz" \
--gender "testdata/gender_classification.txt" \
--cov "testdata/hg38.1kb.chr-19-22-mean_coverage.txt"
or run from the test profile
nextflow run main.nf -profile test,standard
# Step 1 : Make index
nextflow run main.nf \
--step 1 \
--project "1kgp_subset_test" \
--bedgz "testdata/hg38.1kb.chr-19-22.baits.bed.gz"
# Step 2 : Bait read count
nextflow run main.nf \
--step 2 \
--project "1kgp_subset_test" \
--design "testdata/1kg_CEU_7_samples_subset.csv" \
--indexb "results/1kgp_subset_test/index.bed"
# Step 3 : Gender QC
nextflow run main.nf \
--step 3 \
--project "1kgp_subset_test" \
--bindir "results/1kgp_subset_test/bin" \
--index_tab "results/1kgp_subset_test/index_tab.txt"
# Step 4 : logR-ratio calculation
nextflow run main.nf \
--step 4 \
--batch_size 4 \
--target_size 4 \
--project "1kgp_subset_test" \
--bindir "results/1kgp_subset_test/bin" \
--index_tab "results/1kgp_subset_test/index_tab.txt"
# Step 5 : log2 rbin file conversion
nextflow run main.nf \
--step 5 \
--batch_size 4 \
--target_size 4 \
--project "1kgp_subset_test" \
--bindir "results/1kgp_subset_test/bin" \
--cordir "results/1kgp_subset_test/cor" \
--gender "testdata/gender_classification.txt" \
--index_tab "results/1kgp_subset_test/index_tab.txt"
# Step 6 : HMM call
nextflow run main.nf \
--step 6 \
--batch_size 4 \
--target_size 4 \
--project "1kgp_subset_test" \
--rbindir "results/1kgp_subset_test/rbin" \
--cordir "results/1kgp_subset_test/cor" \
--gender "testdata/gender_classification.txt" \
--index_tab "results/1kgp_subset_test/index_tab.txt" \
--cov "testdata/hg38.1kb.chr-19-22-mean_coverage.txt"
# Step 7 : Create Samplefile
nextflow run main.nf \
--step 7 \
--project "1kgp_subset_test" \
--rbindir results/1kgp_subset_test/rbin
# Step 8 : Create cbin files
nextflow run main.nf \
--step 8 \
--project "1kgp_subset_test" \
--rbindir results/1kgp_subset_test/rbin \
--index_tab results/1kgp_subset_test/index_tab.txt \
--samplefile results/samplefile.txt \
-resume