Commit dca41bff authored by David Trudgian's avatar David Trudgian

Merge branch 'CI' into 'master'

Basic CI setup

See merge request !2
parents 91cd945b c9b0ac50
Pipeline #2939 passed with stages
in 3 minutes and 3 seconds
# Run our tests against a specific version of astrocyte
before_script:
- module load astrocyte/0.1.0
stages:
- check
- test
# This performs validation of the astrocyte_pkg.yml file
astrocyte_check:
stage: check
script:
- astrocyte_cli check "$CI_PROJECT_DIR"
# This runs the workflow with test data and does a simple
# check for the expected output files
astrocyte_test:
stage: test
script:
- cd "$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 "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_peaks.bed"
- test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_peaks.xls"
- test -s "$CI_PROJECT_DIR/workflow/output/G1E_ER4_CTCT_chr9.fastq.sam.gz.bam_bwa_nomodel_summits.bed"
# This verifies we can install the shiny vizapp dependencies, set the vizapp
# running and make at least a connection to it.
astrocyte_shiny:
stage: test
script:
- astrocyte_cli shiny-prepare "$CI_PROJECT_DIR"
- 'timeout 10 astrocyte_cli shiny "$CI_PROJECT_DIR" &'
- sleep 5
- unset http_proxy
- unset all_proxy
- wget "http://127.0.0.1:8123"
......@@ -57,6 +57,8 @@ workflow_modules:
# file - A single file from user data
# files - One or more files from user data
# select - A selection from a list of values
# multiselect - One or more selections from a list of values
#
# required: true/false, must the parameter be entered/chosen?
# description: A user friendly description of the meaning of the parameter
#
......@@ -107,7 +109,7 @@ workflow_parameters:
# The workflow must publish all final output into $baseDir
# Name of the R module that the vizapp will run against
vizapp_r_module: 'R/3.2.1-intel'
vizapp_r_module: 'R/3.4.1-gccmkl'
# List of any CRAN packages, not provided by the modules, that must be made
# available to the vizapp
......@@ -115,7 +117,13 @@ vizapp_cran_packages:
- shiny
- shinyFiles
# # List of any Bioconductor packages, not provided by the modules, that must be made
# List of any Bioconductor packages, not provided by the modules, that must be made
# available to the vizapp
vizapp_bioc_packages:
- chipseq
-
# List of any packages to install from GitHub using devtools, that must be
# made availavle to the vizapp
vizapp_github_packages:
-
......@@ -33,9 +33,6 @@ index_name = file(params.index).name
// Output - pair of fastq & generated sai file into the alignments channel
process bwa_aln {
// Tell Nextflow we will use 32 cpus here for BWA
cpus 32
input:
file fastq_file from fastqs
......@@ -57,9 +54,6 @@ process bwa_aln {
// Output - .sam.gz into the samfiles channel, and baseDir/output
process bwa_samse {
// bwa samse will use a single cpu core
cpus 1
// Publish the outputs we create here into the workflow output directory
publishDir "$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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