From fcb0102b8f1172efac2576aee731eb4d95497c97 Mon Sep 17 00:00:00 2001
From: ticlla <monicaroxana.ticllaccenhua@unibas.ch>
Date: Sun, 24 Nov 2019 20:26:26 +0100
Subject: [PATCH] add local rule to make report after MetaPhlAn2 rule has
completed
---
Snakefile | 21 ++++++++++++++++++++-
1 file changed, 20 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 825f6e0..9dd1b51 100644
--- a/Snakefile
+++ b/Snakefile
@@ -103,6 +103,7 @@ localrules:
StrainPhlAn,
rawQC_make_report,
preQC_make_report,
+ MetaPhlAn2_make_report,
PhlAnProf_make_report
##----------------------------------------------------------------------------##
## Run entire workflow
@@ -194,9 +195,27 @@ rule preQC_make_report:
--report {params.report_path} \
-s {params.workflow_dir}/Snakefile preQC) &>{log}
'''
+
+rule MetaPhlAn2_make_report:
+ output:
+ temp(touch(OUT_DIR+'/logs/metaphlan2_make_report.done'))
+ log:
+ OUT_DIR+'/logs/MetaPhlAn2_make_report.log'
+ params:
+ report_path = OUT_DIR+'/MetaPhlAn2_report.html',
+ workdir = workdir_path,
+ workflow_dir = workflow_path
+ shell:
+ '''
+ (snakemake \
+ --directory={params.workdir} \
+ --report {params.report_path} \
+ -s {params.workflow_dir}/Snakefile MetaPhlAn2) &>{log}
+ '''
+
rule PhlAnProf_make_report:
output:
- temp(touch(OUT_DIR+'/logs/preQC_make_report.done'))
+ temp(touch(OUT_DIR+'/logs/phlanprof_make_report.done'))
log:
OUT_DIR+'/logs/PhlAnProf_make_report.log'
params:
--
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