diff --git a/frangiPANe/snakefiles/generate_jupyter_book.smk b/frangiPANe/snakefiles/generate_jupyter_book.smk index 50438ec8c942cbe0bbfecf280bd71d2ac9c2bf5d..38c35ce54ab96b41f08fad2e0c30a4698f217d2d 100644 --- a/frangiPANe/snakefiles/generate_jupyter_book.smk +++ b/frangiPANe/snakefiles/generate_jupyter_book.smk @@ -6,13 +6,8 @@ rule generate_jupyter_book: output: jb_file=f"{ frangipane_obj.path_output }/report/frangiPANe_stats.ipynb" log: - output = f"{frangipane_obj.path_logs}/report/log.o", - error = f"{frangipane_obj.path_logs}/report/log.e" - params: - out_dir= frangipane_obj.path_output, - fastq_dir=frangipane_obj.path_fastq, - group_file=frangipane_obj.path_group, - ref_file=frangipane_obj.path_reference_file, - vec_file=frangipane_obj.path_univec, + output = f"{frangipane_obj.path_logs}/report/jupyterBook.o", + error = f"{frangipane_obj.path_logs}/report/jupyterBook.e" + script: f"{ frangipane_obj.snakemake_scripts }/generate_jb_frangiPANe.py" diff --git a/frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py b/frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py index 44df54a6e3ba21032fe696f23f3d41240c2eeaa7..ae43f00fdc26a548db22ee4892366a75c107cf02 100644 --- a/frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py +++ b/frangiPANe/snakemake_scripts/generate_jb_frangiPANe.py @@ -12,13 +12,13 @@ jb_output = snakemake.output.jb_file # TODO26/11 : use class snakecdysis dico = { - "out_dir" : snakemake.params.out_dir, - "fastq_dir" : snakemake.params.fastq_dir, - "group_file" : snakemake.params.group_file, - "ref_file" : snakemake.params.ref_file, - "vec_file" : snakemake.params.vec_file, - "ref_png" : snakemake.input.png, - "ref_csv" : snakemake.input.csv + "ref_png" : snakemake.input.ref_png, + "ref_csv" : snakemake.input.ref_csv + #"out_dir": snakemake.params.out_dir, + #"fastq_dir": snakemake.params.fastq_dir, + #"group_file": snakemake.params.group_file, + #"ref_file": snakemake.params.ref_file, + #"vec_file": snakemake.params.vec_file, } with open(jb_input, "r", encoding="utf-8") as notebook_file: