diff --git a/README.md b/README.md index 82bf2c5b2e6d1ee8f03cf05b60bb380dd32b2b07..9f4ea2a23c256be8bdbc92dbc3dd9783f71a5455 100644 --- a/README.md +++ b/README.md @@ -475,17 +475,12 @@ intersectionApproach: To run the pipeline, the correct Snakefile (Snakefile_noCTL.smk) should be used: - -<<<<<<< HEAD `snakemake -s Snakefile_noCTL.smk --use-apptainer --apptainer-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1` or using Snakemake Profile: `snakemake -s Snakefile_noCTL.smk --workflow-profile profile/` -======= -`snakemake -s Snakefile_noCTL.smk --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1` ->>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1 ### ATAC-seq mode @@ -507,7 +502,7 @@ Then fill the [config_atac.yaml](https://gitlab.pasteur.fr/hub/ePeak/-/blob/mast All the other features of the standard epeak pipeline are still available (preprocessing including specific quality control, peak annotation and differential analysis, etc.). -<<<<<<< HEAD + To run the pipeline, the correct Snakefile (Snakefile_atac.smk) should be used: @@ -516,12 +511,6 @@ To run the pipeline, the correct Snakefile (Snakefile_atac.smk) should be used: or using Snakemake Profile: `snakemake -s Snakefile_atac.smk --workflow-profile profile/` -======= -To run the pipeline, the correct Snakefile (Snakefile_atac) should be used: - - -`snakemake -s Snakefile_atac.smk --use-singularity --singularity-args "-B '$HOME'" --cluster-config config/cluster_config.json --cluster "sbatch --mem={cluster.ram} --cpus-per-task={threads} " -j 200 --nolock --cores 1` ->>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1 @@ -662,10 +651,9 @@ Run it in a cluster environment via this standard command line: ---- + # Authors -<<<<<<< HEAD * Rachel Legendre (@rlegendr), Research engineer Institut Pasteur * MaÃĢlle Daunesse, Research engineer Institut Pasteur * Adrien Pain, Research engineer Institut Pasteur @@ -679,18 +667,6 @@ Run it in a cluster environment via this standard command line: * Meije MathÊ, Rouen University M2 student * Victoire Baillet, Research engineer Institut Pasteur -======= -* Rachel Legendre (@rlegendr), Institut Pasteur Paris -* MaÃĢlle Daunesse, Institut Pasteur Paris -* Adrien Pain, Institut Pasteur Paris -* Hugo Varet, Institut Pasteur Paris -* Claudia Chica, Institut Pasteur Paris ->>>>>>> 6541328aef7a6535be7fba6a630f83dc48a610c1 - -# Contributors - -* Luc Jouneau, INRAE, Jouy-en-Josas -* Amina Alioua, intern M2 Institut Pasteur Paris # How to cite ePeak ?