Usage	Requirement

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Use slivar on a VCF file to:

• annotate (added in the INFO field, if -g option of slivar is used).
  
• add familial relationship information (added in the INFO field, if --trio, --family-expr, --group-exp, --sample-expr option of slivar is used).
  
• filter (line, i.e., variant removal, according to quality, family criteria, etc.).

• Use nextflow DSL1. To install DSL1 and use it when DSL2 is already installed, see these java and nextflow instructions. This allows to install the nextflow-dls1 command, used below.

• The code uses these following commands of slivar (see this slivar webpage for details):

  slivar expr --js ${fun} -g ${annot1} -g ${annot2} --vcf ${vcf} --ped ${ped} ${sample_expr} ${pedigree_expr} ${filter} -o "res.vcf"
  slivar tsv --ped ${ped} -s ${tsv_sample} ${tsv_info} res.vcf > res.tsv
  

  
  Thus, pay attention with the family_expr, sample and info parameters in the nextflow.config file.

The dataset used in the nextflow.config file, as example, is available at https://zenodo.org/records/10723664.

Installation of:
nextflow DSL1
Graphviz, sudo apt install graphviz for Linux ubuntu
Apptainer

• Mount a server if required:

DRIVE="Z" # change the letter to fit the correct drive
sudo mkdir /mnt/share
sudo mount -t drvfs $DRIVE: /mnt/share

Warning: if no mounting, it is possible that nextflow does nothing, or displays a message like:

Launching `main.nf` [loving_morse] - revision: d5aabe528b
/mnt/share/Users

• Run the following command from where the main.nf and nextflow.config files are (example: \wsl$\Ubuntu-20.04\home\gael):

nextflow-dsl1 run main.nf -c nextflow.config

with -c to specify the name of the config file used.

Run the following command from where you want the results:

nextflow-dsl1 run gael-millot/slivar_vcf_extraction # github, or nextflow-dsl1 run http://github.com/gael-millot/slivar_vcf_extraction
nextflow-dsl1 run -hub pasteur gmillot/slivar_vcf_extraction -r v1.0.0 # gitlab

Copy-paste this after having modified the EXEC_PATH variable:

EXEC_PATH="/pasteur/helix/projects/BioIT/gmillot/slivar_vcf_extraction" # where the bin folder of the main.nf script is located
export CONF_BEFORE=/opt/gensoft/exe # on maestro

export JAVA_CONF=java/13.0.2
export JAVA_CONF_AFTER=bin/java # on maestro
export APP_CONF=apptainer/1.3.5
export APP_CONF_AFTER=bin/apptainer # on maestro
export GIT_CONF=git/2.39.1
export GIT_CONF_AFTER=bin/git # on maestro
export GRAPHVIZ_CONF=graphviz/2.42.3
export GRAPHVIZ_CONF_AFTER=bin/graphviz # on maestro

MODULES="${CONF_BEFORE}/${JAVA_CONF}/${JAVA_CONF_AFTER},${CONF_BEFORE}/${APP_CONF}/${APP_CONF_AFTER},${CONF_BEFORE}/${GIT_CONF}/${GIT_CONF_AFTER}/${GRAPHVIZ_CONF}/${GRAPHVIZ_CONF_AFTER}"
cd ${EXEC_PATH}
chmod 755 ${EXEC_PATH}/bin/*.*
module load ${JAVA_CONF} ${APP_CONF} ${GIT_CONF} ${GRAPHVIZ_CONF}

Modify the second line of the code below, and run from where the main.nf and nextflow.config files are (which has been set thanks to the EXEC_PATH variable above):

HOME_INI=$HOME
HOME="${HELIXHOME}/slivar_vcf_extraction/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/slivar_vcf_extraction/, for instance. See NFX_HOME in the nextflow software script
nextflow-dsl1 run main.nf -c nextflow.config
HOME=$HOME_INI

Modify the first and third lines of the code below, and run (results will be where the EXEC_PATH variable has been set above):

VERSION="v1.0"
HOME_INI=$HOME
HOME="${HELIXHOME}/slivar_vcf_extraction/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/slivar_vcf_extraction/, for instance. See NFX_HOME in the nextflow software script
nextflow-dsl1 run gael-millot/slivar_vcf_extraction -r $VERSION -c $HOME/nextflow.config #github, or nextflow-dsl1 run http://github.com/gael-millot/slivar_vcf_extraction -r $VERSION -c $HOME/nextflow.config
nextflow-dsl1 run -hub pasteur gmillot/slivar_vcf_extraction -r $VERSION -c $HOME/nextflow.config # gitlab
HOME=$HOME_INI

Unknown error accessing project `gmillot/slivar_vcf_extraction` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/slivar_vcf_extraction

Purge using:

rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot*

WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2Fslivar_vcf_extraction

Contact Gael Millot (distant repository is not public).

permission denied

Use chmod to change the user rights. Example linked to files in the bin folder:

chmod 755 bin/*.*

An example of results obtained with the dataset is present at this address: https://zenodo.org/records/10723664/files/slivar_vcf_extraction_1709139998.zip

The different releases are tagged here

This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose. See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.

Not yet published

Freddy Cliquet, GHFC, Institut Pasteur, Paris, France

Gael A. Millot, Hub, Institut Pasteur, Paris, France

The developers & maintainers of the mentioned softwares and packages, including:

• Slivar
• Nextflow
• Apptainer
• Docker
• Gitlab
• Bash
• Ubuntu

Special acknowledgement to Brent Pedersen, Utrecht, The Netherlands, for the release of slivar.

• In the nextflow.config file, downgrade apptainer -> singularity because does not work otherwise.

• In the nextflow.config file, upgrade singularity -> apptainer.

• Dataset and results are in zenodo.
• Transfert into github.

README improved.

Compression added, tsv file optional

Everything