Merge pull request #428 from /issues/422-add-ftp-as-option

Add ftp as input option (resolves #422)

Author: jvivian

src/toil_scripts/bwa_alignment/README.md

@@ -85,7 +85,7 @@ Run a variety of samples locally
     # BWA Alignment Pipeline configuration file
     # This configuration file is formatted in YAML. Simply write the value (at least one space) after the colon.
     # Edit the values in this configuration file and then rerun the pipeline: "toil-bwa run"
-    # URLs can take the form: http://, file://, s3://, gnos://.
+    # URLs can take the form: http://, ftp://, file://, s3://, gnos://.
     # Comments (beginning with #) do not need to be removed. Optional parameters may be left blank
     ##############################################################################################################
     # Required: Reference fasta file

src/toil_scripts/bwa_alignment/bwa_alignment.py

@@ -101,7 +101,7 @@ def generate_config():
         # This configuration file is formatted in YAML. Simply write the value (at least one space) after the colon.
         # Edit the values in this configuration file and then rerun the pipeline: "toil-bwa run"
         #
-        # URLs can take the form: http://, file://, s3://, gnos://
+        # URLs can take the form: http://, ftp://, file://, s3://, gnos://
         # Local inputs follow the URL convention: file:///full/path/to/input
         # S3 URLs follow the convention: s3://bucket/directory/file.txt
         #

src/toil_scripts/exome_variant_pipeline/exome_variant_pipeline.py

@@ -227,7 +227,7 @@ def generate_config():
     # This configuration file is formatted in YAML. Simply write the value (at least one space) after the colon.
     # Edit the values in this configuration file and then rerun the pipeline: "toil-variant run"
     #
-    # URLs can take the form: http://, file://, s3://, gnos://
+    # URLs can take the form: http://, ftp://, file://, s3://, gnos://
     # Local inputs follow the URL convention: file:///full/path/to/input
     # S3 URLs follow the convention: s3://bucket/directory/file.txt
     #
@@ -281,8 +281,8 @@ def generate_manifest():
         #   There are 3 tab-separated columns: UUID, Normal BAM URL, Tumor BAM URL
         #
         #   UUID            This should be a unique identifier for the sample to be processed
-        #   Normal URL      A URL (http://, file://, s3://, gnos://) pointing to the normal bam
-        #   Tumor URL       A URL (http://, file://, s3://, gnos://) pointing to the tumor bam
+        #   Normal URL      A URL (http://, ftp://, file://, s3://, gnos://) pointing to the normal bam
+        #   Tumor URL       A URL (http://, ftp://, file://, s3://, gnos://) pointing to the tumor bam
         #
         #   Examples of several combinations are provided below. Lines beginning with # are ignored.
         #
@@ -371,10 +371,10 @@ def main():
                             help='Path to the (filled in) manifest file, generated with "generate-manifest". '
                                  '\nDefault value: "%(default)s"')
     parser_run.add_argument('--normal', default=None, type=str,
-                            help='URL for the normal BAM. URLs can take the form: http://, file://, s3://, '
+                            help='URL for the normal BAM. URLs can take the form: http://, ftp://, file://, s3://, '
                                  'and gnos://. The UUID for the sample must be given with the "--uuid" flag.')
     parser_run.add_argument('--tumor', default=None, type=str,
-                            help='URL for the tumor BAM. URLs can take the form: http://, file://, s3://, '
+                            help='URL for the tumor BAM. URLs can take the form: http://, ftp://, file://, s3://, '
                                  'and gnos://. The UUID for the sample must be given with the "--uuid" flag.')
     parser_run.add_argument('--uuid', default=None, type=str, help='Provide the UUID of a sample when using the'
                                                                    '"--tumor" and "--normal" option')

src/toil_scripts/rnaseq_cgl/rnaseq_cgl_pipeline.py

@@ -324,7 +324,7 @@ def generate_config():
         # Edit the values in this configuration file and then rerun the pipeline: "toil-rnaseq run"
         # Just Kallisto or STAR/RSEM can be run by supplying only the inputs to those tools
         #
-        # URLs can take the form: http://, file://, s3://, gnos://
+        # URLs can take the form: http://, ftp://, file://, s3://, gnos://
         # Local inputs follow the URL convention: file:///full/path/to/input
         # S3 URLs follow the convention: s3://bucket/directory/file.txt
         #