diff --git a/README.md b/README.md index f752d1c82e80cd4c87a5c482a3323da65dc58ec9..39e07dc4e5b7ddc04ca27aa6c6c6ca5f7d11e23f 100644 --- a/README.md +++ b/README.md @@ -67,10 +67,6 @@ The dataset used in the *nextflow.config* file, as example, is available at http | **Dyslexia.pedigree.txt** | Pedigree file. | | **hg19_grch37p5_chr_size_cumul.txt** | Coordinates of the hg19_grch37p5 Human Genome for the Miami plot | -**example_of_results**: folder containing examples of result obtained with the dataset. -<br /><br /> - See the OUTPUT section for the description of the folder and files. - <br /><br /> ## HOW TO RUN @@ -116,7 +112,7 @@ with -c to specify the name of the config file used. Run the following command from where you want the results: <pre> -nextflow run -hub pasteur gmillot/slivar_vcf_extraction -r v1.0.0 +nextflow run -hub pasteur gmillot/fisher_for_vcf -r v1.0.0 </pre> <br /><br /> @@ -127,7 +123,7 @@ nextflow run -hub pasteur gmillot/slivar_vcf_extraction -r v1.0.0 Copy-paste this after having modified the EXEC_PATH variable: <pre> -EXEC_PATH="/pasteur/zeus/projets/p01/BioIT/gmillot/slivar_vcf_extraction" # where the bin folder of the main.nf script is located +EXEC_PATH="/pasteur/zeus/projets/p01/BioIT/gmillot/fisher_for_vcf" # 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 @@ -152,7 +148,7 @@ Modify the second line of the code below, and run from where the *main.nf* and * <pre> HOME_INI=$HOME -HOME="${ZEUSHOME}/slivar_vcf_extraction/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/slivar_vcf_extraction/, for instance. See NFX_HOME in the nextflow software script +HOME="${ZEUSHOME}/fisher_for_vcf/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/fisher_for_vcf/, for instance. See NFX_HOME in the nextflow software script trap '' SIGINT nextflow run --modules ${MODULES} main.nf -c nextflow.config HOME=$HOME_INI @@ -167,9 +163,9 @@ Modify the first and third lines of the code below, and run (results will be whe <pre> VERSION="v1.0" HOME_INI=$HOME -HOME="${ZEUSHOME}/slivar_vcf_extraction/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/slivar_vcf_extraction/, for instance. See NFX_HOME in the nextflow software script +HOME="${ZEUSHOME}/fisher_for_vcf/" # $HOME changed to allow the creation of .nextflow into /$ZEUSHOME/fisher_for_vcf/, for instance. See NFX_HOME in the nextflow software script trap '' SIGINT -nextflow run --modules ${MODULES} -hub pasteur gmillot/slivar_vcf_extraction -r $VERSION -c $HOME/nextflow.config +nextflow run --modules ${MODULES} -hub pasteur gmillot/fisher_for_vcf -r $VERSION -c $HOME/nextflow.config HOME=$HOME_INI trap SIGINT </pre> @@ -179,7 +175,7 @@ trap SIGINT #### Message 1 ``` -Unknown error accessing project `gmillot/slivar_vcf_extraction` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/slivar_vcf_extraction +Unknown error accessing project `gmillot/fisher_for_vcf` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/fisher_for_vcf ``` Purge using: @@ -189,7 +185,7 @@ rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot* #### Message 2 ``` -WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2Fslivar_vcf_extraction +WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2Ffisher_for_vcf ``` Contact Gael Millot (distant repository is not public).