Added in cleanup as well and new structure.

.gitlab-ci.yml

 variables:
   GIT_DEPTH: 5
-  GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_CONCURRENT_ID/$CI_PROJECT_NAME/$CI_PIPELINE_ID
+  GIT_CLONE_PATH: $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME/$CI_PIPELINE_ID/$CI_CONCURRENT_ID/$CI_JOB_ID/
 
 
 before_script:
@@ -16,6 +16,7 @@ stages:
   - single
   - multiple
   - skip
+  - cleanup
 
 user_configuration:
   stage: unit
@@ -29,6 +30,8 @@ astrocyte:
   - module unload nextflow
   - cd ..
   - astrocyte_cli validate chipseq_analysis
+  after_script:
+    - rm -rf work/
 
 single_end_mouse:
   stage: single
@@ -37,6 +40,9 @@ single_end_mouse:
   script:
   - nextflow run workflow/main.nf --astrocyte true
   - pytest -m singleend
+  after_script:
+    when: on_success
+      - rm -rf work/
 
 paired_end_human:
   stage: single
@@ -47,6 +53,9 @@ paired_end_human:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
   - pytest -m pairedend
+  after_script:
+    when: on_success
+      - rm -rf work/
 
 single_end_single_control:
   stage: single
@@ -57,6 +66,9 @@ single_end_single_control:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
   - pytest -m singlecontrol
+  after_script:
+    when: on_success
+      - rm -rf work/
 
 single_end_diff:
   stage: multiple
@@ -68,6 +80,9 @@ single_end_diff:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
   - pytest -m singleend
   - pytest -m singlediff
+  after_script:
+    when: on_success
+      - rm -rf work/
 
 paired_end_diff:
   only:
@@ -77,6 +92,9 @@ paired_end_diff:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false
   - pytest -m pairedend
   - pytest -m paireddiff
+  after_script:
+    when: on_success
+      - rm -rf work/
 
 single_end_skip:
   stage: skip
@@ -85,3 +103,13 @@ single_end_skip:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true --skipPlotProfile true --astrocyte false
   - pytest -m singleskip_true
+  after_script:
+    when: on_success
+      - rm -rf work/
+
+
+cleanup_job:
+  stage: cleanup
+  script:
+    - cd $CI_BUILDS_DIR/$CI_RUNNER_SHORT_TOKEN/$CI_PROJECT_NAME
+    - rm -fr $CI_PIPELINE_ID/