Commit c9b0ac50 authored by David Trudgian's avatar David Trudgian

Need test data to download to run test

parent 8eba4bb8
Pipeline #2937 passed with stages
in 3 minutes and 3 seconds
......@@ -17,6 +17,8 @@ astrocyte_check:
astrocyte_test:
stage: test
script:
- cd "$CI_PROJECT_DIR/test_data"
- sh fetch_test_data.sh
- astrocyte_cli test "$CI_PROJECT_DIR"
- test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam"
- test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_peaks.bed"
......
......@@ -33,9 +33,6 @@ index_name = file(params.index).name
// Output - pair of fastq & generated sai file into the alignments channel
process bwa_aln {
// Tell Nextflow we will use 32 cpus here for BWA
cpus 32
input:
file fastq_file from fastqs
......@@ -57,9 +54,6 @@ process bwa_aln {
// Output - .sam.gz into the samfiles channel, and baseDir/output
process bwa_samse {
// bwa samse will use a single cpu core
cpus 1
// Publish the outputs we create here into the workflow output directory
publishDir "$baseDir/output", mode: 'copy'
......@@ -86,10 +80,9 @@ process sam2bam {
// Tell Nextflow picard will only use one cpu.
// We are allocating 32GB to java though, so tell
// We are allocating 16GB to java though, so tell
// Nextflow so it can assign the task appropriately.
cpus 1
memory '32GB'
memory '16GB'
// Publish the outputs we create here into the workflow output directory
publishDir "$baseDir/output", mode: 'copy'
......@@ -102,7 +95,7 @@ process sam2bam {
"""
module add picard/1.127
java -Xmx32G -jar \$PICARD/picard.jar SortSam \
java -Xmx16G -jar \$PICARD/picard.jar SortSam \
INPUT="${sam_file}" \
OUTPUT="${sam_file.name}.bam" \
SORT_ORDER=coordinate \
......
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