From 2a00f4d57a6355e47fd7146d1c1aeb10c3d0a702 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Thu, 28 Nov 2019 11:24:48 +0100
Subject: [PATCH] in2p3.pbs: update pbs to use training_dataset.nf
---
src/in2p3.pbs | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/src/in2p3.pbs b/src/in2p3.pbs
index 60f342a3..ac6d0869 100644
--- a/src/in2p3.pbs
+++ b/src/in2p3.pbs
@@ -20,10 +20,12 @@ NF=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
# change to your username
SCRATCH=/sps/lbmc/lmodolo/
# change to your project / pipeline !
-PIPELINE=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.nf
+PIPELINE=${SCRATCH}/nextflow/src/training_dataset.nf
# change to your project / pipeline !
-CONFIG=${SCRATCH}/nextflow/src/nf_modules/kallisto/indexing.config
+CONFIG=${SCRATCH}/nextflow/src/training_dataset.config
${NF} ${PIPELINE} -c ${CONFIG} -profile ccin2p3 \
---fasta "${SCRATCH}/nextflow/data/tiny_dataset/fasta/tiny_v2.fasta" \
+--fasta "${SCRATCH}/nextflow/data/genome.fa" \
+--fastq_single "${SCRATCH}/nextflow/data/*_R1.fastq.gz" \
+--chromosome "X" --start 5305683 --stop 5333928 -resume
-w "${SCRATCH}"
--
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