Remove unnecessary intermediate outputs from publish and remove unit tests for them

workflow/main.nf

@@ -73,7 +73,6 @@ references = params.references
 process checkDesignFile {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda'
 
   input:
@@ -309,7 +308,6 @@ process count310 {
 process versions {
 
   tag "${name}"
-  publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
   module 'python/3.6.1-2-anaconda:pandoc/2.7:multiqc/1.7'
 
   input:
@@ -357,4 +355,4 @@ process multiqc {
     multiqc -c ${multiqcConf} .
     """
 
-}
+}
\ No newline at end of file

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_count/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.count211
-def test_count211_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count301
-def test_count301_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count302
-def test_count302_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
-
-@pytest.mark.count310
-def test_count310_design():
-    assert os.path.exists(os.path.join(test_output_path, 'design.checked.csv'))
\ 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_count/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.count211
-def test_count211_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.count301
-def test_count301_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.count302
-def test_count302_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.count310
-def test_count310_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

[Gervaise Henry]

Analogous to cellranger_mkfastq#35 (closed)