From 55939a1e63147869523ccab9cd6124d09a002539 Mon Sep 17 00:00:00 2001
From: Shaman <shaman.narayanasamy@uni.lu>
Date: Wed, 25 Mar 2015 11:28:43 +0100
Subject: [PATCH] changed output names
---
docker/Dockerfile | 3 ---
rules/Analysis/MGMT.rules | 13 +++++++++----
rules/Analysis/master.rules | 12 ++++++------
3 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 2d23ae5..cf54df6 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -171,9 +171,6 @@ RUN cd /home/imp/lib \
&& cd megahit \
&& make
-## KronaTools
-
-
######################
# ship pipeline code #
######################
diff --git a/rules/Analysis/MGMT.rules b/rules/Analysis/MGMT.rules
index 5c45afa..f9a7ed1 100644
--- a/rules/Analysis/MGMT.rules
+++ b/rules/Analysis/MGMT.rules
@@ -541,14 +541,16 @@ rule ANALYSIS_KRONA_PLOT_MG:
"{U_OUT}/pwy2hierarchy.txt",
"{AN_OUT}/MG.gene_depth.avg",
"{AN_OUT}/MG.gene.len",
+ output:
"{AN_OUT}/results/MG.gene_kegg_krona.txt",
"{AN_OUT}/results/MG.gene_kegg_krona.html"
shell:
"""
echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
- python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {input[4]}
- ktImportText -o {input[5]} {input[4]}"
+ python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {output[0]}
+ ktImportText -o {output[1]} {output[0]}"
"""
+
rule ANALYSIS_KRONA_PLOT_MT:
log:
AN_LOG
@@ -560,11 +562,14 @@ rule ANALYSIS_KRONA_PLOT_MT:
"{U_OUT}/pwy2hierarchy.txt",
"{AN_OUT}/MT.gene_depth.avg",
"{AN_OUT}/MT.gene.len",
+ output:
"{AN_OUT}/results/MT.gene_kegg_krona.txt",
"{AN_OUT}/results/MT.gene_kegg_krona.html"
shell:
"""
echo "[x] PLOT KRONA `date +"%Y/%m/%d %H:%M:%S"`" >> {log}
- python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {input[4]}
- ktImportText -o {input[5]} {input[4]}"
+ python {SRCDIR}/genes.to.kronaTable.py -i {input[0]} -m {input[1]} -H {input[2]} -c {input[3]} -L {input[3]} -o {output[0]}
+ ktImportText -o {output[1]} {output[0]}"
"""
+
+
diff --git a/rules/Analysis/master.rules b/rules/Analysis/master.rules
index fce86d5..822e63d 100644
--- a/rules/Analysis/master.rules
+++ b/rules/Analysis/master.rules
@@ -17,12 +17,12 @@ def analysis_output_files():
"MT.variants.isec.vcf.gz",
"MGMT.assembly.length.txt",
"MGMT.assembly.gc_content.txt",
- "MT.assembly.coverage_coverage.txt",
- "MT.assembly.coverage_depth.txt",
- "MT.assembly.coverage_flagstat.txt",
- "MG.assembly.coverage_coverage.txt",
- "MG.assembly.coverage_depth.txt",
- "MG.assembly.coverage_flagstat.txt",
+ "MT.assembly.contig_coverage.txt",
+ "MT.assembly.contig_depth.txt",
+ "MT.assembly.contig_flagstat.txt",
+ "MG.assembly.contig_coverage.txt",
+ "MG.assembly.contig_depth.txt",
+ "MG.assembly.contig_flagstat.txt",
"MGMT.vizbin.points",
"MGMT.vizbin.filtered.fa",
"MGMT.vizbin.with-contig-names.points"], dir=AN_OUT)
--
GitLab