testing singularity

astrocyte_pkg.yml

@@ -161,6 +161,7 @@ workflow_parameters:
       - [ '/project/shared/bicf_workflow_ref/human/GRCh38', 'Human GRCh38']
       - [ '/project/shared/bicf_workflow_ref/human/GRCh37', 'Human GRCh37']
       - [ '/project/shared/bicf_workflow_ref/mouse/GRCm38', 'Mouse GRCm38']
+      - [ '/project/shared/bicf_workflow_ref/mouse/GRCm39', 'Mouse GRCm39']
     required: true
     description: |
       Reference genome for alignment

nextflow.config

@@ -6,32 +6,38 @@ process {
   clusterOptions = '--hold --no-kill'
   queue = '128GB,256GB,256GBv1'
   withLabel: trim {
-    container = 'trim_galore.sif'
+    container = 'goalconsortium/trim_galore:1.0.9'
   }
-  withLabel: dnaalign {
-     container = 'dna_alignment.sif'
+  withLabel: abra2 {
+    container = 'goalconsortium/abra2:1.0.9'
   }
   withLabel: profiling_qc {
-    container = 'profiling_qc.sif'
+    container = 'goalconsortium/profiling_qc:1.0.9'
+  }
+  withLabel: dnaalign {
+     container = 'goalconsortium/dna_alignment:1.0.9'
+  }
+  withLabel: variantcalling  {
+    container = 'goalconsortium/variantcalling:1.0.9'
+  }
+  withLabel: structuralvariant {
+     container = 'goalconsortium/structuralvariant:1.1.2'
   }
   withLabel: starfusion {
-    container = 'starfusion.sif'
+    container = 'goalconsortium/starfusion:1.0.9'
   }
   withLabel: ralign {
-    container = 'rna_alignment.sif'
+    container = 'goalconsortium/rna_alignment:1.0.9'
   }
   withLabel: geneabund {
-    container = 'rna_gene_abundance.sif'
-  }
-  withLabel: rnaseqstat {
-    container = 'rnaseq_dea.sif'
+    container = 'goalconsortium/rna_gene_abundance:1.1.3'
   }
 }
 
 singularity {
   enabled = true
   runOptions='--no-home --cleanenv'
-  cacheDir = '/project/shared/bicf_workflow_ref/seqprg/singularity/'
+  cacheDir="$PWD"
 }
 
 trace {
@@ -57,9 +63,9 @@ env {
 }
 
 manifest {
-  homePage = 'https://git.biohpc.swmed.edu/ngsclialab/school'
-  description = 'School is a collection of genomics analysis workflows that are used for detecting single nucleotide variants (SNVs), insertions/deletions (indels), copy number variants (CNVs) and translocations from RNA and DNA sequencing.  These workflows have been validated in a CLIA laboratory at UTSW'
+  homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq'
+  description = 'RNA sequencing gene abundance analysi'
   mainScript = 'rna.nf'
   version = '1.0.0'
-  nextflowVersion = '>=0.31.0'
+  nextflowVersion = '>=20.01.0'
 }

testing/human_pe_test/run_test.sh

+#!/bin/bash
+
+module load nextflow/20.01.0 singularity/3.5.3
+base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
+datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
+
+nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design  ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis

testing/mouse_se_test/run_test.sh

+#!/bin/bash
+
+module load nextflow/20.01.0 singularity/3.5.3
+base='/project/BICF/BICF_Core/s166458/rnaseq_astrocyte'
+datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
+
+nextflow -C ${base}/nextflow.config run -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html ${base}/workflow/main.nf --design  ${datadir}/mouse_se.design.txt --input ${datadir} --pairs se --output analysis

testing/run_all_tests.sh

+#!/bin/bash
+
+baseDir="`dirname \"$0\"`"
+
+cd ${baseDir}/mouse_se_test/
+sbatch -p 32GB,super run_test.sh
+cd ${baseDir}/human_pe_test/
+sbatch -p 32GB,super run_test.sh