From 80a1657802cdb757c7cdbe54e0630bcdd07b9a86 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 15 May 2019 15:35:08 +0200
Subject: [PATCH] improve comment of nextflow.pbs
---
src/conda_packages.sh | 1 +
src/nextflow.pbs | 12 ++++++++----
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/src/conda_packages.sh b/src/conda_packages.sh
index 5c39b0cb..f4be84f8 100644
--- a/src/conda_packages.sh
+++ b/src/conda_packages.sh
@@ -57,4 +57,5 @@ install_env file handle 0.1.1 file handle
install_env ncdu 1.13 ncdu
install_env picard 2.18.11 picard
install_env sambamba 0.6.7 sambamba
+install_env subread 1.6.4 subread
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
index d1fede85..4cb6e04c 100644
--- a/src/nextflow.pbs
+++ b/src/nextflow.pbs
@@ -17,9 +17,13 @@
NF_VERSION=19.04
NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-PIPELINE=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.nf
-CONFIG=/sps/lbmc/common/nextflow/src/nf_modules/kallisto/indexing.config
+# change to your username
+SCRATCH=/sps/lbmc/<user>/
+# change to your project / pipeline !
+PIPELINE=${SCRATCH}/<project>/src/<pipeline>.nf
+# change to your project / pipeline !
+CONFIG=${SCRATCH}/<project>/src/<pipeline>.config
${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
---fasta "/sps/lbmc/common/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
--w "/sps/lbmc/<user>/"
+--fasta "${SCRATCH}/<project>/data/fasta" \
+-w "${SCRATCH}"
--
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