Make most updates except last one

.gitlab-ci.yml

@@ -4,16 +4,17 @@ before_script:
   - pip install --user pytest-pythonpath==0.7.1 pytest-cov==2.5.1
   - module load nextflow/20.01.0
   - module load singularity/3.5.3
-  - mkdir -p test_data/simple1
-  - mkdir -p test_data/simple2
-  - mkdir -p test_data/simple3
-  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/* test_data/simple1/
-  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple2/* test_data/simple2/
-  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple3/* test_data/simple3/
+  - mkdir -p test_data/cellranger1bcl
+  - mkdir -p test_data/cellranger2bcl
+  - mkdir -p test_data/spaceranger1bcl
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/cellranger1bcl/* test_data/cellranger1bcl/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/cellranger2bcl/* test_data/cellranger2bcl/
+  - ln -sfn /project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/spaceranger1bcl/* test_data/spaceranger1bcl/
 
 stages:
   - astrocyte
-  - simple
+  - cellranger
+  - spaceranger
 
 astrocyte_check:
   stage: astrocyte
@@ -26,11 +27,11 @@ astrocyte_check:
     when:
       - always
 
-simple_1FC:
-  stage: simple
+cellranger1bcl:
+  stage: cellranger
   script:
-    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
-    ##- pytest -m simple1
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/cellranger1bcl/*.tar.gz" --designFile "test_data/cellranger1bcl/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
+    ##- pytest -m cellranger1bcl
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -43,11 +44,11 @@ simple_1FC:
     when:
       - always
 
-simple_2FC:
-  stage: simple
+cellranger2bcl:
+  stage: cellranger
   script:
-    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
-    ##- pytest -m simple2
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "cellranger" --bcl "test_data/cellranger2bcl/*.tar.gz" --designFile "test_data/cellranger2bcl/cellranger-tiny-bcl-simple-1_2_0.csv" --ci true
+    ##- pytest -m cellranger2bcl
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -60,11 +61,11 @@ simple_2FC:
     when:
       - always
 
-simple_3FC:
-  stage: simple
+spaceranger1bcl:
+  stage: spaceranger
   script:
-    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "spaceranger" --bcl "test_data/simple3/*.tar.gz" --designFile "test_data/simple3/spaceranger-tiny-bcl-simple-1.0.0.csv" --ci true
-    ##- pytest -m simple3
+    - nextflow run workflow/main.nf -profile biohpc,cluster --ranger "spaceranger" --bcl "test_data/spaceranger1bcl/*.tar.gz" --designFile "test_data/spaceranger1bcl/spaceranger-tiny-bcl-simple-1.0.0.csv" --ci true
+    ##- pytest -m spaceranger1bcl
   artifacts:
     name: "$CI_JOB_NAME"
     when: always

CHANGELOG.md

@@ -3,6 +3,7 @@
 * Add flag to select cellranger vs spaceranger
 * Adjust versions to take into account multiple 10x-Ranger softwares
 * Remove countDesign process
+* Spaceranger V1.2.0 update
 
 **Background**
 * Update scripts to reflect spaceranger or cellranger input

README.md

@@ -42,19 +42,19 @@ To Run:
 * Available parameters:
   * **-profile**
     * what environments to run on, available: `biohpc`, `local`, `cluster`, `aws`, `ondemand`, `spot`
-    * eg: ```-profile biohpc,cluster``` to run on BioHPC in cluster mode
-    * eg: ```-profile aws,ondemand``` to run on AWS on a on-demand queue
+    * eg: `-profile biohpc,cluster` to run on BioHPC in cluster mode
+    * eg: `-profile aws,ondemand` to run on AWS on a on-demand queue
   * **--name**
     * run name, puts outputs in a directory with this name
-    * eg: ```--name 'test'```
+    * eg: `--name 'test'`
   * **--ranger**
     * select the 10x ranger being run.
-    * eg: ```--ranger 'cellranger'``` to run cellranger mkfastq
-    * eg: ```--ranger 'spaceranger'``` to run spaceranger mkfastq
+    * eg: `--ranger 'cellranger'` to run cellranger mkfastq
+    * eg: `--ranger 'spaceranger'` to run spaceranger mkfastq
   * **--bcl**
     * base call files (tarballed [*.tar] +/- gunzipping [*.tar.gz] from a sequencing of 10x single-cell expereiment, supports pigr parallelization)
     * there can be multiple basecall files, but they all will be demultiplexed by the same design file
-    * eg: ```--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'```
+    * eg: `--bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz'`
   * **--designFile**
     * path to design file (csv format) location
     * column 1 = "Lane" (number of lanes to demultiplex, **\*** for all lanes)
@@ -64,13 +64,13 @@ To Run:
     * [Current sample barcode IDs](https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv)
     * can have repeated "Sample" if there are multiple fastq R1/R2 pairs for the samples
     * can be downloaded [HERE](https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/master/docs/design.csv)
-    * eg: ```--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'```
+    * eg: `--designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple/cellranger-tiny-bcl-simple-1_2_0.csv'`
   * **--mask**
     * add a base mask if the sequencing strategy doesn't match the requirements of 10x Genomics
-    * eg: ```--mask '--use-bases-mask=Y\*,I8n\*,n\*,Y\*'```
+    * eg: `--mask '--ignore-dual-index --use-bases-mask=Y\*,I8n\*,n\*,Y\*'`
   * **--outDir**
     * optional output directory for run
-    * eg: ```--outDir 'test'```
+    * eg: `--outDir 'test'`
 * FULL EXAMPLE:
   ```
   nextflow run workflow/main.nf -profile biohpc,cluster --name 'test' --ranger 'cellranger' --bcl '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-1_2_0.tar.gz' --designFile '/project/shared/bicf_workflow_ref/workflow_testdata/cellranger/cellranger_mkfastq/simple1/cellranger-tiny-bcl-simple-1_2_0.csv' --outDir 'test'

workflow/main.nf

@@ -76,6 +76,7 @@ process trackStart {
       "sessionId": "${workflow.sessionId}", \
       "pipeline": "cellranger_mkfastq", \
       "pipelineVersion": "${pipelineVersion}", \
+      "10x-ranger": ${params.ranger}, \
       "start": "${workflow.start}", \
       "astrocyte": ${params.astrocyte}, \
       "status": "started", \
@@ -213,7 +214,7 @@ process spaceranger_mkfastq {
   tag "${bcl.simpleName}"
   publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
   queue '128GB,256GB,256GBv1,384GB'
-  module 'spaceranger/1.1.0:bcl2fastq/2.19.1'
+  module 'spaceranger/1.2.0:bcl2fastq/2.19.1'
 
   input:
     file versions_spacerangerScript

workflow/tests/test_mkfastq.py

@@ -14,15 +14,15 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 		'/../output/'
 
-@pytest.mark.simple1
-def test_simple1_mkfastq():
+@pytest.mark.cellranger1bcl
+def test_cellranger1bcl_mkfastq():
     assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0', 'outs'))
 
-@pytest.mark.simple2
-def test_simple2_mkfastq():
+@pytest.mark.cellranger2bcl
+def test_cellranger2bcl_mkfastq():
     assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0-1', 'outs'))
     assert os.path.exists(os.path.join(test_output_path, 'mkfastq', 'cellranger-tiny-bcl-1_2_0-2', 'outs'))
 
-@pytest.mark.simple3
-def test_simple3_mkfastq():
+@pytest.mark.spaceranger1bcl
+def test_spaceranger1bcl_mkfastq():
     assert os.path.exists(os.path.join(test_output_path, 'spaceranger_mkfastq', 'mkfastq_spaceranger-tiny-bcl-1', 'outs'))

workflow/tests/test_multiqc.py

@@ -14,14 +14,14 @@ import os
 test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/multiqc/run/'
 
-@pytest.mark.simple1
-def test_simple1_multiqc():
+@pytest.mark.cellranger1bcl
+def test_cellranger1bcl_multiqc():
     assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
 
-@pytest.mark.simple2
-def test_simple2_multiqc():
+@pytest.mark.cellranger2bcl
+def test_cellranger2bcl_multiqc():
     assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))
 
-@pytest.mark.simple3
-def test_simple3_multiqc():
+@pytest.mark.spaceranger1bcl
+def test_spaceranger1bcl_multiqc():
     assert os.path.exists(os.path.join(test_output_path, 'multiqc_report.html'))