From 8fc16bd712bf131c7d273123d0ceeea3f03d5db3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 26 Apr 2021 16:23:17 +0200
Subject: [PATCH] kallisto: fix singleend reads table
---
src/.docker_modules/kb/0.26.0/Dockerfile | 7 +++++++
src/.docker_modules/kb/0.26.0/docker_init.sh | 4 ++++
src/nf_modules/kallisto/main.nf | 2 +-
3 files changed, 12 insertions(+), 1 deletion(-)
create mode 100644 src/.docker_modules/kb/0.26.0/Dockerfile
create mode 100755 src/.docker_modules/kb/0.26.0/docker_init.sh
diff --git a/src/.docker_modules/kb/0.26.0/Dockerfile b/src/.docker_modules/kb/0.26.0/Dockerfile
new file mode 100644
index 00000000..920dc9e0
--- /dev/null
+++ b/src/.docker_modules/kb/0.26.0/Dockerfile
@@ -0,0 +1,7 @@
+FROM python:3.9-slim
+
+ENV KB_VERSION="0.26.0"
+
+RUN pip3 install kb-python==${KB_VERSION}
+
+CMD [ "bash" ]
diff --git a/src/.docker_modules/kb/0.26.0/docker_init.sh b/src/.docker_modules/kb/0.26.0/docker_init.sh
new file mode 100755
index 00000000..347c10e4
--- /dev/null
+++ b/src/.docker_modules/kb/0.26.0/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/kb:0.26.0
+docker build src/.docker_modules/kb/0.26.0 -t 'lbmc/kb:0.26.0'
+docker push lbmc/kb:0.26.0
diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index b4d59dca..8d3fe1d3 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -62,6 +62,6 @@ process mapping_fastq {
mkdir ${file_prefix}
kallisto quant -i ${index} -t ${task.cpus} --single \
${params.mapping_fastq} -o ${file_prefix} \
- ${reads} &> ${file_prefix}_kallisto_mapping_report.txt
+ ${reads[0]} &> ${file_prefix}_kallisto_mapping_report.txt
"""
}
--
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