From e1928a57fb5f6f42cc294dd50106c9c9ee2e9665 Mon Sep 17 00:00:00 2001
From: "julie.orjuela" <julie.orjuela@ird.fr>
Date: Tue, 26 Mar 2024 11:07:20 +0100
Subject: [PATCH] comment sample_info into the snakefile and minor modifs on
readme
---
README.md | 69 +++++++++++++++++++-------------------
RNAja/snakefiles/Snakefile | 6 ++--
2 files changed, 37 insertions(+), 38 deletions(-)
diff --git a/README.md b/README.md
index 5b4c485..0cc0a7a 100644
--- a/README.md
+++ b/README.md
@@ -47,40 +47,6 @@ Install RNAja in cluster mode using **singularity** container from rnaja_utiliti
Please run command line 'RNAja edit_cluster_config' before the first run of RNAja see https://forge.ird.fr/phim/rnaja-pipeline/README.md and configure by default threads and memory resources.
-## 2. Running a datatest
-
-Running test with a datatest from RNAja_utilities in a repertory TEST
-
-```bash
- RNAja test_install --help
- RNAja test_install -d TEST
-```
-
-### 2.1 Running your data in LOCAL mode
-
-launching suggested command line done by RNAja, in LOCAL mode:
-
-```bash
- RNAja run_local --help
- RNAja run_local -t 8 -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
-```
-
-In local mode, it's possible to allocate threads to some rules using `--set-threads` snakemake argument such as
-
-```
- RNAja run_local -t 8 -c TEST/data_test_config.yaml --set-threads hisat2_index=4 hisat2_map_paired=2
-```
-
-### 2.2 Running your data in CLUSTER mode
-
-Now you can launch suggested command line done by RNAja in `cluster` mode BUT before you need to configurate cluster parameters running command line `RNAja edit_cluster_config` before the first run and modify threads, ram, node and computer resources.
-RNAja does a copy of `cluster_config.yaml` file into your home `"/home/$USER/.config/rnaja_pipeline/cluster_config.yaml"`
-
-```bash
- RNAja run_cluster --help
- RNAja edit_cluster_config
-```
-
Feel free to modify resources (RAM, CPU number and partition) using the rules names found above.
```
@@ -124,8 +90,41 @@ rule stringtie_discovery
```
+## 2. Running a datatest
+
+Running a test to be sure of RNAja installation. RNAja `test_install` download an available dataset from a distant server (RNAja_utilities i-Trop). Pipeline tests are launched in a repertory (option -d DIR_NAME) created by RNAja.
+
+```bash
+ RNAja test_install --help
+ RNAja test_install -d TEST
+```
+
+### 2.1 Running your data in LOCAL mode
+
+launching suggested command line done by RNAja, in LOCAL mode:
+
+```bash
+ RNAja run_local --help
+ RNAja run_local -t 8 -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
+```
+
+In local mode, it's possible to allocate threads to some rules using `--set-threads` snakemake argument such as
+
+```
+ RNAja run_local -t 8 -c TEST/data_test_config.yaml --set-threads hisat2_index=4 hisat2_map_paired=2
+```
+
+### 2.2 Running your data in CLUSTER mode
+
+Now you can launch suggested command line done by RNAja in `cluster` mode BUT before you need to configurate cluster parameters running command line `RNAja edit_cluster_config` before the first run and modify threads, ram, node and computer resources.
+RNAja does a copy of `cluster_config.yaml` file into your home `"/home/$USER/.config/rnaja_pipeline/cluster_config.yaml"`
+
+```bash
+ RNAja run_cluster --help
+ RNAja edit_cluster_config
+```
-If singularity was selected in installation of RNAja, it could be needed to give argument `--singularity-args \"--bind $HOME\"` to Snakemake, by using :
+If singularity was selected in installation of RNAja, it could be needed to give argument `--singularity-args \"--bind $HOME\"` to RNAja, by using :
```bash
RNAja run_cluster --help
diff --git a/RNAja/snakefiles/Snakefile b/RNAja/snakefiles/Snakefile
index ea5b915..6b7a2e7 100644
--- a/RNAja/snakefiles/Snakefile
+++ b/RNAja/snakefiles/Snakefile
@@ -18,7 +18,7 @@ cluster_config = RNAja_obj.cluster_config
# print(RNAja_obj.export_use_yaml)
# print for debug:
#
-pp(RNAja_obj)
+#pp(RNAja_obj)
# print(tools_config)
#exit()
@@ -29,7 +29,7 @@ log_dir = Path(config["DATA"]["output_dir"]+"/LOGS/").resolve()
annotation_path = Path(config["DATA"]["annotation"]).resolve()
reference_path = Path(config["DATA"]["reference"]).resolve()
reference_basename = Path(config["DATA"]["reference"]).stem
-samplefile = Path(config["DATA"]["sample_info"]).resolve()
+#samplefile = Path(config["DATA"]["sample_info"]).resolve()
fastq_dir = Path(config["DATA"]["fastq_dir"]).resolve()
# Change workdir to output path (slurm logs append on outdir)
@@ -573,7 +573,7 @@ rule diff_exp_analysis:
threads: get_threads('diff_exp_analysis',4)
input:
gcsv=rules.prepDE_stringtie_table.output.gcsv,
- sample_info=config["DATA"]["sample_info"],
+ #sample_info=config["DATA"]["sample_info"],
#de_comparisons_file=config["DATA"]["files"]["de_comparisons_file"],
gtf_file=config["DATA"]["annotation"],
params:
--
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