Finishes python workflow

Author: Hexotical

toil/cwl/cwl_input.yaml

@@ -3,12 +3,12 @@ quant: quant
 libtype: A
 fqOne: 
   class: File
-  location: /home/hexotical/bioinformatics-workflows/toil/cwl/data/reads_1.fq
+  location: /home/luk/Desktop/bioinformatics-workflows/test_data/reads_1.fq.gz
   format: http://edamontology.org/format_1930
 fqTwo: 
   class: File
-  location: /home/hexotical/bioinformatics-workflows/toil/cwl/data/reads_2.fq
+  location: /home/luk/Desktop/bioinformatics-workflows/test_data/reads_2.fq.gz
   format: http://edamontology.org/format_1930
 transcriptome:
   class: File
-  location: /home/hexotical/bioinformatics-workflows/toil/cwl/data/transcriptome.fa
+  location: /home/luk/Desktop/bioinformatics-workflows/test_data/transcriptome.fa

toil/python/draft.py

@@ -32,7 +32,7 @@ def run(self, fileStore):
 
         fpath = fileStore.readGlobalFile(self.reads, userPath=os.path.join(tempDir, os.path.basename(self.reads)))
         cmd = f'zcat "{fpath}" | fastqc stdin:readsone'
-
+        #cmd = f'ls -lha .. && ls -lha && echo {fpath} && pwd'
         generate_docker_bashscript_file(temp_dir=tempDir, docker_dir=tempDir, globs=[], cmd=cmd, job_name='FastQCone')
 
         # apiDockerCall() with demux=True returns a tuple of bytes objects (stdout, stderr).
@@ -242,4 +242,5 @@ def run(self, fileStore):
 
         fileStore.start(fastqc_job_1)
 
-#/home/hexotical/bioinformatics-workflows/toil/python/index.tar.gz
+#/home/hexotical/bioinformatics-workflows/toil/python/index.tar.gz
+#/home/luk/venv/lib/python3.8/site-packages/toil/leader.py