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 0000000000000000000000000000000000000000..920dc9e075e6fa54b4e290e194ba7b60507338c3 --- /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 0000000000000000000000000000000000000000..347c10e4aa1ac05d130b860b10024b016fdc4eef --- /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 b4d59dcae6c3be7054bad65b14176c49e4ae322d..8d3fe1d3a9bbdd1435863f93ab0b74c1d7bcd994 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 """ }