Merge branch 'CI' into 'master'

Basic CI setup

See merge request biohpc/astrocyte_example_chipseq!2

.gitlab-ci.yml

+# 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"
+

astrocyte_pkg.yml

@@ -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:
+  -
+

workflow/main.nf

@@ -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 \