From e96b93da89e6daceabd12ba7cfb5b9f52ab1aea5 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.fr>
Date: Sat, 6 Jan 2024 18:09:43 +0100
Subject: [PATCH] integrating fasta plot
---
frangiPANe/snakefiles/generate_jupyter_book.smk | 11 +++--------
.../snakemake_scripts/generate_jb_frangiPANe.py | 14 +++++++-------
2 files changed, 10 insertions(+), 15 deletions(-)
diff --git a/frangiPANe/snakefiles/generate_jupyter_book.smk b/frangiPANe/snakefiles/generate_jupyter_book.smk
index 50438ec..38c35ce 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 44df54a..ae43f00 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:
--
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