From 8e1d221094854c8c3d529d559856fa3444bef939 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 6 Mar 2023 10:28:06 +0100
Subject: [PATCH] add output dir for kmdiff

---
 src/mbelari_diff.slurm         | 2 +-
 src/mlongespiculosa_diff.slurm | 2 +-
 src/mspiculigera_diff.slurm    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mbelari_diff.slurm b/src/mbelari_diff.slurm
index 31c5ffc..3f51bf3 100644
--- a/src/mbelari_diff.slurm
+++ b/src/mbelari_diff.slurm
@@ -14,4 +14,4 @@ KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img
 WORK=$(pwd)
 
 # kmdiff count
-${KMDIFF} diff -d ${WORK}/results/mbelari_counts/ -1 1 -2 1 -t 32
+${KMDIFF} diff -d ${WORK}/results/mbelari_counts/ -1 1 -2 1 -t 32 -o ${WORK}/results/mbelari_diff
diff --git a/src/mlongespiculosa_diff.slurm b/src/mlongespiculosa_diff.slurm
index 7c2eb9c..2a3a758 100644
--- a/src/mlongespiculosa_diff.slurm
+++ b/src/mlongespiculosa_diff.slurm
@@ -14,4 +14,4 @@ KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img
 WORK=$(pwd)
 
 # kmdiff count
-${KMDIFF} diff -d ${WORK}/results/mlongespiculosa_counts/ -1 7 -2 2 -t 32
+${KMDIFF} diff -d ${WORK}/results/mlongespiculosa_counts/ -1 7 -2 2 -t 32 -o ${WORK}/results/mlongespiculosa_diff
diff --git a/src/mspiculigera_diff.slurm b/src/mspiculigera_diff.slurm
index 5b561ac..8308f71 100644
--- a/src/mspiculigera_diff.slurm
+++ b/src/mspiculigera_diff.slurm
@@ -15,4 +15,4 @@ KMDIFF="/Xnfs/abc/charliecloud_bin/ch-run -b /scratch /Xnfs/abc/charliecloud/img
 WORK=$(pwd)
 
 # kmdiff count
-${KMDIFF} diff -d ${WORK}/results/mspiculigera_counts/ -1 1 -2 1 -t 32
+${KMDIFF} diff -d ${WORK}/results/mspiculigera_counts/ -1 1 -2 1 -t 32 -o ${WORK}/results/mspiculigera_diff
-- 
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