nextflow version 23.10.0.5889
- see
/docs/Installation_guidelines.md
for full instructions.
The workflow is called 'break-sites'
- Once the git repository has been pulled, in the project directory,
make a 'run' directory and cd into this dir.
This will compartmentalise results
mkdir run cd run
- From the 'run' directory, USAGE:
nextflow run ../main.nf
- This will produce a work directory and a dated results directory with all output files.
CON-MP2C0C8L:~/scripts/broken-strings/run$ nextflow run ../main.nf N E X T F L O W ~ version 23.10.0 Launching `../main.nf` [jovial_fermi] DSL2 - revision: c8f5bde496 executor > local (49) [0c/64671b] process > break_sites:FILTER_Q30 (q30_filtering) [100%] 16 of 16 ✔ [48/d75667] process > break_sites:INTERSECT (intersect_q30_files) [100%] 16 of 16 ✔ [c9/6894a8] process > break_sites:NORMALISED (normalise) [100%] 16 of 16 ✔ [95/7d4565] process > break_sites:NEATEN (neaten) [100%] 1 of 1 ✔ CON-MP2C0C8L:~/scripts/broken-strings/run$ ls results_2023-10-22-15:44:07 work
- Results
dalebridges@CON-MP2C0C8L:~/scripts/broken-strings/run$ ls results_2023-10-22-16\:46\:46/ Plot-DBS_normalised_count_results.html Sample13.breakends.bed.counts Sample2.breakends.bed.filtered Sample6.breakends.bed.filtered.intersected Sample1.breakends.bed.counts Sample13.breakends.bed.filtered Sample2.breakends.bed.filtered.intersected Sample6.counts.txt Sample1.breakends.bed.filtered Sample13.breakends.bed.filtered.intersected Sample2.counts.txt Sample7.breakends.bed.counts Sample1.breakends.bed.filtered.intersected Sample13.counts.txt Sample3.breakends.bed.counts Sample7.breakends.bed.filtered Sample1.counts.txt Sample14.breakends.bed.counts Sample3.breakends.bed.filtered Sample7.breakends.bed.filtered.intersected Sample10.breakends.bed.counts Sample14.breakends.bed.filtered Sample3.breakends.bed.filtered.intersected Sample7.counts.txt Sample10.breakends.bed.filtered Sample14.breakends.bed.filtered.intersected Sample3.counts.txt Sample8.breakends.bed.counts Sample10.breakends.bed.filtered.intersected Sample14.counts.txt Sample4.breakends.bed.counts Sample8.breakends.bed.filtered Sample10.counts.txt Sample15.breakends.bed.counts Sample4.breakends.bed.filtered Sample8.breakends.bed.filtered.intersected Sample11.breakends.bed.counts Sample15.breakends.bed.filtered Sample4.breakends.bed.filtered.intersected Sample8.counts.txt Sample11.breakends.bed.filtered Sample15.breakends.bed.filtered.intersected Sample4.counts.txt Sample9.breakends.bed.counts Sample11.breakends.bed.filtered.intersected Sample15.counts.txt Sample5.breakends.bed.counts Sample9.breakends.bed.filtered Sample11.counts.txt Sample16.breakends.bed.counts Sample5.breakends.bed.filtered Sample9.breakends.bed.filtered.intersected Sample12.breakends.bed.counts Sample16.breakends.bed.filtered Sample5.breakends.bed.filtered.intersected Sample9.counts.txt Sample12.breakends.bed.filtered Sample16.breakends.bed.filtered.intersected Sample5.counts.txt all.counts.txt Sample12.breakends.bed.filtered.intersected Sample16.counts.txt Sample6.breakends.bed.counts results.txt Sample12.counts.txt Sample2.breakends.bed.counts Sample6.breakends.bed.filtered
Sample#.breakends.bed.counts
the original raw filesSample#.counts.txt
there are the individual counts that are collected by collectFile directive in 'main.nf'Sample#.breakends.bed.filtered
q30 filtered filesSample#.breakends.bed.filtered.intersected
is the intersected results with the chr21_AsiSI_sites.t2t.bed fileall.counts.txt
is the combination results Sample#.counts.txt resultsresults.txt
is all.counts.txt with an additional header and simple ordering, it is the final file that is used for plottingPlot-DBS_normalised_count_results.html
produces the plot of normalised counts rounded to the nearest1. Unless the number falls below 0.5 then this is captured as uncertain and coloured blue.
Each of the module code in the bin
folder can be run independently
Usage:
python3 filter_q30.py {sample}.breakends.bed -o ${sample}.filtered > ${sample}.counts
Usage:
bash normalised_counts.sh {sample_name}.breakends.bed {sample_name}.breakends.bed.filtered.intersected
- see 'plot/README.md' for additional details. Usage:
python3 plot_samples_normalised_counts_rounded.py
- see
bedtools
below for installation Usage: - https://bedtools.readthedocs.io/en/latest/content/quick-start.html#use-bedtools
.gitignore
files and folder to ignore e.g., run folder.
main.nf
runs the workflow
nextflow.config
sets the paramaters, processes etc. for workflow execution
- links to all files in the
configs
directory.README.md
this file.
- in-house developed scripts
- all raw sample bed files
- chr21 intersect file
configs for additional nextflow settings as called by 'nextflow.config'
files for building docker container
Answers to questions, Discussion points, Installation_guidelines and some troubleshooting.
The main module file with all of the workflow processes to run. This calls the script and tool commands. (The Brain!)
the plot details for running independently and the final result.
NOTE:
- All dependencies have been built into the docker file in the docker folder.
- If running independent of docker set
docker enabled=false
in theconfigs/docker.config
file - bedtools will need to be installed within the local environment
- Plotly will need to be installed for Python3 to run the plots
ubuntu:20.04
python 3.8.10 requirements: argparse plotly==5.17.0
sudo apt-get install bedtools
- see
/docs/Installation_guidelines.md
for full instructions.
Docker version 20.10.21, build 20.10.21-0ubuntu1~20.04.1
- see
/docs/Installation_guidelines.md
for full instructions.
- See
docs/Troubleshooting.md
for common errors and solutions