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assemble
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assemble
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#!/bin/bash
# exit script if one command fails
set -o errexit
# exit script if Variable is not set
set -o nounset
INPUT=/bbx/input/biobox.yaml
OUTPUT=/bbx/output
METADATA=/bbx/metadata
# Since this script is the entrypoint to your container
# you can access the task in `docker run task` as the first argument
TASK=$1
# Ensure the biobox.yaml file is valid
validate-biobox-file \
--input ${INPUT} \
--schema /schema.yaml \
mkdir -p ${OUTPUT}
# Parse the read locations from this file
READS=$(yaml2json < ${INPUT} \
| jq --raw-output '.arguments[] | select(has("fastq")) | .fastq[].value ' \
| tr '\n' ' ')
#create temporary directory in /tmp
TMP_DIR=$(mktemp -d)
# Use grep to get $TASK in /Taskfile
CMD=$(egrep ^${TASK}: /Taskfile | cut -f 2 -d ':')
if [[ -z ${CMD} ]]; then
echo "Abort, no task found for '${TASK}'."
exit 1
fi
# if /bbx/metadata mounted create log.txt
if [ -d "$METADATA" ]; then
CMD="($CMD) >& $METADATA/log.txt"
fi
# Run the given task with eval.
# Eval evaluates a String as if you would use it on a command line.
eval ${CMD}
# This command writes yaml into the biobox.yaml until the EOF symbol is reached
cat << EOF > ${OUTPUT}/biobox.yaml
version: 0.9.0
arguments:
- fasta:
- id: contigs1
value: assembly-contigs.fa
type: contigs
EOF