Merge branch 'master' into cwl-outputs-doc-#137

README.md

@@ -14,7 +14,7 @@ contact [John Vivian]([email protected]).
 ### Appendix
 
 - [Dependencies and Installation](#dependencies-and-installation)
-- [Quickstart](#general-usage)
+- [Quickstart](#quickstart)
 
 For detailed information and troubleshooting, see the [Wiki](https://github.com/BD2KGenomics/toil-rnaseq/wiki)
 - [Workflow Inputs](https://github.com/BD2KGenomics/toil-rnaseq/wiki/Workflow-Inputs)
@@ -37,11 +37,6 @@ This workflow takes RNA sequencing reads (fastq / BAM) as input and outputs the
 │   ├── fusion.txt
 │   └── run_info.json
 ├── QC
-│   ├── bamQC
-│   │   ├── readDist.txt
-│   │   ├── readDist.txt_PASS_qc.txt
-│   │   ├── rnaAligned.out.md.sorted.geneBodyCoverage.curves.pdf
-│   │   └── rnaAligned.out.md.sorted.geneBodyCoverage.txt
 │   ├── fastQC
 │   │   ├── R1_fastqc.html
 │   │   ├── R1_fastqc.zip
@@ -62,9 +57,9 @@ This workflow takes RNA sequencing reads (fastq / BAM) as input and outputs the
     ├── rsem_genes.results
     └── rsem_isoforms.results
 ```
-If the user selects options such as `save-star-bam`, or `wiggle`, additional files will appear in the output directory:
+If the user selects options such as `save-bam`, or `wiggle`, additional files will appear in the output directory:
 
-- SAMPLE.sorted.bam OR SAMPLE.sortedByCoord.md.bam if `bamQC` step is enabled.
+- SAMPLE.sorted.bam
 - SAMPLE.wiggle.bg
 
 The output tarball is prepended with the unique name for the sample (e.g. SAMPLE.tar.gz). 

setup.py

@@ -5,7 +5,7 @@
 kwargs = dict(
     name='toil-rnaseq',
     version=version,
-    description="UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline",
+    description="UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq workflow",
     author='UCSC Computational Genomics Lab',
     author_email='[email protected]',
     url="https://github.com/BD2KGenomics/toil-lib",
@@ -14,19 +14,19 @@
     package_dir={'': 'src'},
     packages=find_packages('src'),
     entry_points={
-        'console_scripts': ['toil-rnaseq = toil_rnaseq.rnaseq_cgl_pipeline:main',
+        'console_scripts': ['toil-rnaseq = toil_rnaseq.toil_rnaseq:main',
                             'toil-rnaseq-inputs = toil_rnaseq.input_generation:main']})
 
 
 setup(**kwargs)
 
 
 print("\n\n"
-      "Thank you for installing the UC Santa Cruz Computuational Genomics Lab RNA-seq pipeline\n"
-      "If you want to run this Toil-based pipeline on a cluster in a cloud, please install Toil\n "
+      "Thank you for installing the UC Santa Cruz Computuational Genomics Lab RNA-seq workflow\n"
+      "If you want to run this Toil-based workflow on a cluster in a cloud, please install Toil\n "
       "with the appropriate extras. For example, To install AWS/EC2 support for example, run"
       "\n\n"
       "pip install toil[aws,mesos]%s"
       "\n\n"
       "For more information, please refer to Toil's documentation:\n"
-      "http://toil.readthedocs.io/en/latest/installation.html")
+      "https://toil.readthedocs.io")

src/toil_rnaseq/input_generation.py

@@ -8,8 +8,9 @@
 
 from toil.job import Job
 from toil.lib.docker import dockerCall
-from toil_lib.files import move_files
-from toil_lib.urls import download_url
+
+from utils.files import move_files
+from utils.urls import download_url
 
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(__name__)
@@ -150,7 +151,7 @@ def hera_index(job, args):
 
 def main():
     """
-    Generate inputs / indices for tools used in the toil-rnaseq pipeline
+    Generate inputs / indices for tools used in the toil-rnaseq workflow
 
     Create inputs for:
         - STAR
@@ -182,7 +183,7 @@ def main():
     # Toil wrapper options
     parser.add_argument('--max-cores', type=int, default=12, help='Maximum number of cores to use')
     parser.add_argument('--work-dir', type=str, default='.', help='Directory to put temporary files')
-    parser.add_argument('--resume', action='store_true', default=False, help='Restarts pipeline')
+    parser.add_argument('--resume', action='store_true', default=False, help='Restarts workflow')
 
     # Flags
     parser.add_argument('--star', action='store_true', default=None, help='Create input for STAR')