Commit 4a723adc authored by Erwan DELAGE's avatar Erwan DELAGE
Browse files

Add hidden configuration file in output directory, correct bug in report

parent 02fca5d5
......@@ -86,7 +86,6 @@ def initialize_pipeline(arguments):
# Prepare fastqc step
prepare_fastqc()
def init_logger():
"""
The logger will register the configuration and steps of the workflow.
......@@ -612,6 +611,8 @@ def format_all_rule():
all_input.append(config["global"]["outdir"] + "/" + LOGFILE)
all_input.append(getOutput("multiqc"))
all_input.append(config["global"]["outdir"] + "/.config.json")
if "denoiser" in config["global"]:
all_input.append(getOutput("summarize_table", "table.qzv"))
all_input.append(getOutput("export_table_tsv", "abundance_table.tsv"))
......@@ -673,6 +674,15 @@ rule log_config:
run:
log_config()
rule export_config_json:
input: json_config_path[1]
output: config["global"]["outdir"] + "/.config.json"
run:
# Export config
with open(output[0], 'w') as outfile:
json.dump(config, outfile, indent=4)
###########################
## FASTQC ##
###########################
......@@ -1286,7 +1296,7 @@ if "denoiser" in config["global"]:
rule build_report:
input :
config=json_config_path[1]
config=outdir + "/.config.json"
output:
outdir + "/report.tar.gz"
shell: """
......
......@@ -128,7 +128,7 @@
<a href="#beta_group_significance">Beta group significance</a>
</li>
{% endif %}
{% if adonis %}
{% if bray_curtis_adonis %}
<li>
<a href="#adonis">Adonis</a>
</li>
......@@ -145,7 +145,7 @@
{% endif %}
{% if deseq2 %}
<li>
<a href="#deseq2">Differential abundance with DESeq2</a>
<a href="#difab-deseq2">Differential abundance with DESeq2</a>
</li>
{% endif %}
<li>
......@@ -373,6 +373,9 @@
<p>Commit number : <b>{{commit_number}}</b></p>
</div>
<div>
<p> microSysMics is hosted on <a href="https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics"> the gitlab of Nantes university</a>. Wiki available <a href="https://gitlab.univ-nantes.fr/bird_pipeline_registry/microSysMics/-/wikis/home">here</a>.</p>
</div>
</div> <!-- bs-docs-section -->
</div> <!-- col-md-10 -->
</div> <!-- row-fluid -->
......@@ -384,4 +387,4 @@
</script>
</html>
\ No newline at end of file
</html>
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