From 94a24ded694e0bf8a8890d6a262e99cb9a97f884 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 22 Nov 2019 13:41:18 +0100
Subject: [PATCH] src/ cleanup .pbs example
---
src/nextflow.pbs | 39 ---------------------------------------
1 file changed, 39 deletions(-)
delete mode 100644 src/nextflow.pbs
diff --git a/src/nextflow.pbs b/src/nextflow.pbs
deleted file mode 100644
index e89d8599..00000000
--- a/src/nextflow.pbs
+++ /dev/null
@@ -1,39 +0,0 @@
-#! /usr/local/bin/bash -l
-#####################################
-# job script example with GE options
-#####################################
-#$ -q demon
-#$ -l demon=1
-#$ -P P_lbmc
-#$ -N nf_pipe
-#$ -o /sps/lbmc/<user>/logs/ # change to your username !
-#$ -e /sps/lbmc/<user>/logs/ # change to your username !
-#$ -r n # relaunch y/n
-#$ -M <email>@ens-lyon.fr # change to your mail !
-#$ -m be ## send an email when the job starts and ends
-#$ -l os=cl7 ## choose OS
-#$ -l sps=1 ## acces /sps directory
-#####################################
-
-# change to your username !
-SCRATCH=/sps/lbmc/<user>/
-# change to your project name !
-PROJECT=<project>
-#change to your project version !
-PIPELINE=<pipeline_name>
-#NF version to user
-NF_VERSION=19.04
-
-
-NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
-NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
-CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
-DATA=${SCRATCH}/${PROJECT}/data
-NF_OPTIONS="-w \"${SCRATCH}/${PROJECT}/work/\" \
--with-report \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html\" \
--with-timeline \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html\" \
--with-dag \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.html\""
-
-${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 ${NF_OPTIONS} \
---fasta "${DATA}/fasta" \
---results "${SCRATCH}/${PROJECT}/results/"
--
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