Commit ed19ffd7 authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Merge branch 'develop' of gitlab.univ-nantes.fr:bird_pipeline_registry/microSysMics into develop

parents d219419f c42b5b32
......@@ -132,6 +132,21 @@
"cutadapt": {
"type": "object"
},
"filter_reads": {
"type": "object",
"properties" : {
"method" : {
"type": "string"
},
"i-database" : {
"type": "string"
}
},
"required": [
"method",
"i-database"
]
},
"fastqc": {
"type": "object"
},
......@@ -165,4 +180,4 @@
"global"
],
"additionalProperties": false
}
\ No newline at end of file
}
......@@ -1218,10 +1218,10 @@ if "denoiser" in config["global"]:
rule evolution_nbreads:
input: getOutput("export_table_tsv", "abundance_table.tsv")
output: getOutput("summarize_table", "plots/evolution_nbreads.tsv")
params: manifest = config["global"]["manifest"],
outdir = config["global"]["outdir"]
params: outdir = config["global"]["outdir"],
config_file = json_config_path[1]
shell: """
python scripts/evolution_nbreads.py {params.manifest} {params.outdir}
python scripts/evolution_nbreads.py {params.outdir} {params.config_file}
"""
##################################
......
......@@ -2,6 +2,7 @@ import pandas as pd
import seaborn as sns
import sys
import json
import matplotlib.pyplot as plt
OUTDIR = sys.argv[1]
CONFIG = sys.argv[2]
......@@ -73,7 +74,9 @@ stats_plot["sample_id"] = stats_plot.index
stats_plot = pd.melt(stats_plot, id_vars="sample_id", value_vars=steps)
stats_plot.columns = ["sample_id", "processing_step", "nb_reads"]
nb_reads_boxplot = sns.boxplot(x="processing_step", y="nb_reads", data=stats_plot)
fig_dims = (15, 6)
fig, ax = plt.subplots(figsize=fig_dims)
nb_reads_boxplot = sns.boxplot(x="processing_step", y="nb_reads", ax = ax, data=stats_plot)
# Export plot
nb_reads_boxplot.figure.savefig(OUTDIR + "/summarize_table/plots/evolution_nbreads.svg")
......
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