Merge branch '35-CleanupOutputs' into 'develop'

Resolve "Cleanup process outputs"

Closes #35

See merge request !56

workflow/main.nf

@@ -36,7 +36,6 @@ references = params.references
 process checkDesignFile {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda'
 
   input:
@@ -63,7 +62,6 @@ process checkDesignFile {
 process untarBCL {
 
   tag "${tar}"
-  publishDir "${outDir}/${task.process}", mode: 'copy'
   module 'pigz/2.4'
 
   input:
@@ -114,7 +112,7 @@ if (bclCount.value == 1) {
   process countDesign {
 
     tag "${name}"
-    publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
+    publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
 
     input:
       file fastqs from cellrangerCount.collect()
@@ -137,7 +135,6 @@ process fastqc {
 
   tag "${bclName}"
   queue 'super'
-  publishDir "${outDir}/misc/${task.process}/${name}/${bclName}", mode: 'copy', pattern: "{*fastqc.zip}"
   module 'fastqc/0.11.5:parallel'
 
   input:
@@ -161,7 +158,6 @@ process fastqc {
 process versions {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
 
   input:

workflow/tests/test_check_design.py

-#!/usr/bin/env python3
-#test_check_design.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/misc/checkDesignFile/run/'
-
-@pytest.mark.simple1
-def test_simple1_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.simple2
-def test_simple2_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))    
\ No newline at end of file

workflow/tests/test_fastqc.py

-#!/usr/bin/env python3
-#test_fastq.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/misc/fastqc/run/'
-
-@pytest.mark.simple1
-def test_simple1_fastqc():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0'))
-
-@pytest.mark.simple2
-def test_simple2_fastqc():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2'))
\ No newline at end of file

workflow/tests/test_untarBCL.py

-#!/usr/bin/env python3
-#test_untarBCL.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/untarBCL/'
-
-@pytest.mark.simple1
-def test_simple1_untarBCL():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0', 'RTAComplete.txt'))
-
-@pytest.mark.simple2
-def test_simple2_untarBCL():
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-1', 'RTAComplete.txt'))
-    assert os.path.exists(os.path.join(test_output_path, 'cellranger-tiny-bcl-1_2_0-2', 'RTAComplete.txt'))
\ No newline at end of file

workflow/tests/test_versions.py

-#!/usr/bin/env python3
-#test_versions.py
-#*
-#* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/blob/develop/LICENSE)
-#* --------------------------------------------------------------------------
-#*
-
-import pytest
-import pandas as pd
-from io import StringIO
-import os
-
-test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/misc/versions/run/'
-
-@pytest.mark.simple1
-def test_simple1_versions():
-    assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
-    assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
-
-@pytest.mark.simple2
-def test_simple2_versions():
-    assert os.path.exists(os.path.join(test_output_path, 'versions_mqc.yaml'))
-    assert os.path.exists(os.path.join(test_output_path, 'references_mqc.yaml'))
\ No newline at end of file