diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5d9a3be3d46027621fc4a0fc7cf88d53079f83a1..eb44569784c41e056da3f7d23181c8a6550f4849 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,34 +2,25 @@
 # Brandi L. Cantarel - 2017
 
 variables:
-  GIT_SUBMODULE_STRATEGY: normal
+  GIT_SUBMODULE_STRATEGY: recursive
 
 before_script:
-  - module load astrocyte/1.0.0
   - module load nextflow/20.01.0
-  - module load singularity/3.5.3
+  - module load singularity/3.0.2
 
 stages:
-  - check
-  - test_human
-  - test_mouse
-
-# This performs validation of the astrocyte_pkg.yml file
-astrocyte_check:
-  stage: check
-  script:
-  - astrocyte_cli check "$CI_PROJECT_DIR" 
+  - integration
 
 test_human:
-  stage: test_human
+  stage: integration
   script:
-    - nextflow run -c workflow/configs/nextflow.config -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
+    - nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline human_timeline.html -with-report human_report.html workflow/main.nf --design  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/design.rnaseq.txt --input  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --output human_output
   artifacts:
     expire_in: 2 days
 
 test_mouse:
-  stage: test_mouse
+  stage: integration
   script:
-    - nextflow run -c workflow/configs/nextflow.config -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html  workflow/main.nf --input  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output
+    - nextflow run -c nextflow.config -with-dag flowchart.png -with-timeline mouse_timeline.html -with-report mouse_report.html  workflow/main.nf --input  /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq --design /project/shared/bicf_workflow_ref/workflow_testdata/rnaseq/mouse_se.design.txt --pairs se --fusion skip --genome /project/shared/bicf_workflow_ref/mouse/GRCm38 --markdups null --output mouse_output
   artifacts:
     expire_in: 2 days
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index 0242dee412031e1290cd19266bcb68035939fcaf..0000000000000000000000000000000000000000
--- a/.gitmodules
+++ /dev/null
@@ -1,3 +0,0 @@
-[submodule "workflow/process_scripts"]
-	path = workflow/process_scripts
-	url = git@git.biohpc.swmed.edu:ngsclialab/process_scripts.git
diff --git a/README.md b/README.md
index 7b6ac564cc5bd18887916764ae90aecf1086a67b..93561bb73bf59d23fbe58af7c6ef5555b9f96105 100644
--- a/README.md
+++ b/README.md
@@ -69,7 +69,7 @@ module load nextflow/20.01.0 singularity/3.5.3
 base=$repoClonedDirectory
 datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
 
-nextflow -C ${base}/workflow/configs/nextflow.config run ${base}/workflow/main.nf --design  ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
+nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design  ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
 
 ```
 
@@ -80,7 +80,7 @@ module load nextflow/20.01.0 singularity/3.5.3
 base=$repoClonedDirectory
 datadir='/project/shared/bicf_workflow_ref/workflow_testdata/rnaseq'
 
-nextflow -C ${base}/workflow/configs/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
+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
 
 ```
 
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index a7b3480013c7b355b6169b5a7c73bbfd1057c7d0..47962cd4987298242134038d30852a0a66188825 100644
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -20,20 +20,6 @@ description: |
   It implements differential expression analysis, gene set enrichment analysis,
   gene fusion analysis and variant identification using RNASeq data.
 
-# The minimum Astrocyte version that requires to run this workflow. For old pipelines, which do not have this label 
-# a default value of 0.3.1 will be assigned automatically. A request of minimum version less than 0.4.0 will be ignored.
-minimum_astrocyte_version: '0.4.1'
-# The Nextflow version that requires to run this workflow.  For old pipelines, which do not have this label 
-# a default value of 0.31.0 will be assigned automatically. Please make sure the requested nextflow version is available
-# in the module list.
-nextflow_version: '20.01.0'
-# (Optional) The Nextflow config file to use for this workflow. If provided, the file should exist in workflow/configs
-nextflow_config: 'nextflow.config'
-# The container to use for this workflow, none/singularity. If omitted, the default value 'none' will be used.
-container: 'singularity'
-# The version of singularity to use. This is required if container == 'singularity'
-singularity_version: '3.5.3'
-
 
 # -----------------------------------------------------------------------------
 # DOCUMENTATION
@@ -64,22 +50,6 @@ workflow_modules:
   - 'stringtie/1.1.2-intel'
   - 'speedseq/20160506'
   - 'python/2.7.x-anaconda'
-
-# A list of container images requires to run this workflow.
-# Specify full path and version names to ensure reproducability.
-# This keyword is required when 'container' is specified in Astrocyte 0.4.1 and above
-workflow_containers:
-  - docker://goalconsortium/trim_galore:1.0.9
-  - docker://goalconsortium/abra2:1.0.9
-  - docker://goalconsortium/profiling_qc:1.0.9
-  - docker://goalconsortium/dna_alignment:1.0.9
-  - docker://goalconsortium/variantcalling:1.0.9
-  - docker://goalconsortium/structuralvariant:1.1.4
-  - docker://goalconsortium/starfusion:1.0.9
-  - docker://goalconsortium/rna_alignment:1.0.9
-  - docker://goalconsortium/rna_gene_abundance:1.1.3
-  - docker://goalconsortium/rna_statanal:1.1.4
-
 # A list of parameters used by the workflow, defining how to present them,
 # options etc in the web interface. For each parameter:
 #
diff --git a/workflow/configs/nextflow.config b/nextflow.config
similarity index 77%
rename from workflow/configs/nextflow.config
rename to nextflow.config
index c0eec91496b730abec3ee662fc608fab67ebb61b..150748a34379cf059276d0144009eb1943283927 100644
--- a/workflow/configs/nextflow.config
+++ b/nextflow.config
@@ -1,28 +1,27 @@
 params {
        repoDir='/seqprg'
 }
-
 process {
   executor = 'slurm'
   clusterOptions = '--hold --no-kill'
   queue = '128GB,256GB,256GBv1'
   withLabel: trim {
-    container = 'goalconsortium/trim_galore:1.1.3'
+    container = 'goalconsortium/trim_galore:1.0.9'
   }
   withLabel: abra2 {
     container = 'goalconsortium/abra2:1.0.9'
   }
   withLabel: profiling_qc {
-    container = 'goalconsortium/profiling_qc:1.1.3'
+    container = 'goalconsortium/profiling_qc:1.0.9'
   }
   withLabel: dnaalign {
-     container = 'goalconsortium/dna_alignment:1.1.3'
+     container = 'goalconsortium/dna_alignment:1.0.9'
   }
   withLabel: variantcalling  {
-    container = 'goalconsortium/variantcalling:1.1.5'
+    container = 'goalconsortium/variantcalling:1.0.9'
   }
   withLabel: structuralvariant {
-     container = 'goalconsortium/structuralvariant:1.1.4'
+     container = 'goalconsortium/structuralvariant:1.1.2'
   }
   withLabel: starfusion {
     container = 'goalconsortium/starfusion:1.0.9'
@@ -40,13 +39,13 @@ process {
 
 singularity {
   enabled = true
-  runOptions='--no-home --cleanenv --disable-cache'
-  cacheDir = "$baseDir/images/singularity"
+  runOptions='--no-home --cleanenv'
+  singularity.cacheDir="$PWD"
 }
 
 trace {
   enabled = true
-  file = 'trace.txt'
+  file = 'pipeline_trace.txt'
   field = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime'
 }
 
diff --git a/testing/run_human_pe_test.sh b/testing/run_human_pe_test.sh
index ade5af35acd8489732831ce49b85764075781518..e8624c09d8caa4d85134c0c3f2ddbe7f55b9e952 100644
--- a/testing/run_human_pe_test.sh
+++ b/testing/run_human_pe_test.sh
@@ -4,4 +4,4 @@ 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}/workflow/configs/nextflow.config run ${base}/workflow/main.nf --design  ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
+nextflow -C ${base}/nextflow.config run ${base}/workflow/main.nf --design  ${datadir}/design.rnaseq.txt --input ${datadir} --output analysis
diff --git a/testing/run_mouse_se_test.sh b/testing/run_mouse_se_test.sh
index 2d3f06b22f936cb4cffa9387882f97f9b0614b01..2c105e3bcdb151a336dc6e0302704828291c4570 100644
--- a/testing/run_mouse_se_test.sh
+++ b/testing/run_mouse_se_test.sh
@@ -4,4 +4,4 @@ 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}/workflow/configs/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
+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 ${datadir} --pairs se --output analysis
diff --git a/workflow/main.nf b/workflow/main.nf
index c6a508d4c32cc5a440ae464e7bb8d6fd887ac11c..ef33763fcf301bd64566fe467137e4069db5e659 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -23,13 +23,9 @@ indel="$params.genome/GoldIndels.vcf.gz"
 knownindel=file(indel)
 dbsnp=file(dbsnp)
 
-
+repoDir=workflow.projectDir
 if (params.repoDir) {
-  repoDir=params.repoDir
-} else if (workflow.projectDir) {
-  repoDir=workflow.projectDir
-} else {
-  repoDir="$baseDir"
+   repoDir=params.repoDir
 }
 
 // params genome is the directory
@@ -49,8 +45,6 @@ process checkdesignfile {
 	stdout spltnames
 	script:
 	"""
-  # convert dos \\r to unix format
-  sed -i 's/\\x0D\$//' design.ori.txt
 	bash $repoDir/process_scripts/design_file/checkdesignfile.sh ${params.pairs} design.ori.txt
 	"""
 }
@@ -96,15 +90,12 @@ process ralign {
   errorStrategy 'ignore'
   label 'ralign'
   publishDir "$params.output", mode: 'copy'
-  
   input:
   set pair_id, file(fqs) from trimread
-  
   output:
   set pair_id, file("${pair_id}.bam") into aligned
   set pair_id, file("${pair_id}.bam") into aligned2
   file("${pair_id}.alignerout.txt") into hsatout
-  
   script:
   """
   bash $repoDir/process_scripts/alignment/rnaseqalign.sh -a $params.align -p ${pair_id} -r ${index_path} ${fqs}
diff --git a/workflow/process_scripts b/workflow/process_scripts
deleted file mode 160000
index e5e905a0ada2d2a93ff0ed59b2fdf022a56c7464..0000000000000000000000000000000000000000
--- a/workflow/process_scripts
+++ /dev/null
@@ -1 +0,0 @@
-Subproject commit e5e905a0ada2d2a93ff0ed59b2fdf022a56c7464