Merge pull request #609 from MG-RAST/wilke/seqUtil

Wilke/seq util

Author: wilke

CWL/README.md

@@ -2,37 +2,40 @@
 
 This directory contains tool and workflow definitions in CWL. Tests scripts and data go into the Tests and Data directory.
 
-Running tests:
-Download large reference files
+
+
+## Main workflows
+
+- amplicon
+  - amplicon-fasta.workflow.yaml
+  - amplicon-fastq.workflow.yaml
+- assembled
+  - assembled.workflow.cwl
+- metabarcode
+  - metabarcode-fasta.workflow.cwl
+  - metabarcode-fastq.workflow.cwl
+- wgs
+  - wgs-fasta.workflow.cwl
+  - wgs-fastq.job.yaml
+  - wgs-noscreen-fasta.workflow.cwl
+  - wgs-noscreen-fastq.job.yaml
+
+## Running tests
+
+1. Download large reference files for tests and pipeline:
 ```bash
-bash CWL/Inputs/DBs/getpredata.sh
+CWL/Inputs/DBs/getpredata.sh
 ```
 
-Working commands
+
+## Working commands
 ```bash
 cwltool --cachedir .cache2 --no-match-user amplicon-fasta.workflow.cwl amplicon-fasta.job.yaml 
 cwltool --cachedir .cache2 --no-match-user amplicon-fastq.workflow.cwl amplicon-fastq.job.yaml 
 
 ```
 
 
-To check: 
-assembled.workflow.cwl assembled.job.yaml
-metabarcode-fasta.workflow.cwl metabarcode-fasta.job.yaml	
-metabarcode-fastq.workflow.cwl metabarcode-fastq.job.yaml	
-wgs-fasta.workflow.cwl wgs-fasta.job.yaml
-
-
-Errors:
-wgs-fastq.workflow.cwl wgs-fastq.job.yaml
-and 
-wgs-fasta.workflow.cwl  wgs-fasta.job.yaml
 
-Traceback (most recent call last):
-  File "/usr/local/bin/seqUtil", line 372, in <module>
-    subset_seqs(opts.input, opts.list, opts.out, opts.check, opts.minimum)
-  File "/usr/local/bin/seqUtil", line 224, in subset_seqs
-    if len(record.seq) < minimum:
-NameError: global name 'record' is not defined