updates for release

CHANGELOG.md

@@ -0,0 +1,7 @@
+# 2.0.5
+
+* checking if the pem key path exists
+* number of arguments checking relaxed, help is displayed with `--help` or no arguments
+* option to specify either VCF or tar, one is required but not both
+* added optional parameters that specify UUIDs for related GNOS uploads
+* updated docs

README.md

@@ -72,34 +72,53 @@ Note: the variant calling working group has specified ".tbi" rather than ".idx"
 
 The parameters:
 
-    perl gnos_upload_vcf.pl
-       --metadata-urls <URLs_for_specimen-level_aligned_BAM_input_comma_sep>
-       --vcfs <sample-level_vcf_file_path_comma_sep_if_multiple>
-       --vcf-md5sum-files <file_with_vcf_md5sum_comma_sep_same_order_as_vcfs>
-       --vcf-idxs <sample-level_vcf_idx_file_path_comma_sep_if_multiple>
-       --vcf-idx-md5sum-files <file_with_vcf_idx_md5sum_comma_sep_same_order_as_vcfs>
-       --tarballs <tar.gz_non-vcf_files_comma_sep_if_multiple>
-       --tarball-md5sum-files <file_with_tarball_md5sum_comma_sep_same_order_as_tarball>
-       --outdir <output_dir>
-       --key <gnos.pem>
-       --upload-url <gnos_server_url>
-       [--workflow-src-url <http://... the source repo>]
-       [--workflow-url <http://... the packaged SeqWare Zip>]
-       [--workflow-name <workflow_name>]
-       [--workflow-version <workflow_version>]
-       [--seqware-version <seqware_version_workflow_compiled_with>]
-       [--description-file <file_path_for_description_txt>]
-       [--study-refname-override <study_refname_override>]
-       [--analysis-center-override <analysis_center_override>]
-       [--pipeline-json <pipeline_json_file>]
-       [--qc-metrics-json <qc_metrics_json_file>]
-       [--timing-metrics-json <timing_metrics_json_file>]
-       [--make-runxml]
-       [--make-expxml]
-       [--force-copy]
-       [--skip-validate]
-       [--skip-upload]
-       [--test]
+    USAGE: 'perl gnos_upload_vcf.pl
+     --metadata-urls <URLs_for_specimen-level_aligned_BAM_input_comma_sep>
+     --outdir <output_dir>
+     --key <gnos.pem>
+     --upload-url <gnos_server_url>
+     # you must specify --vcfs, --vcf-md5sum-files, --vcf-idxs, and --vcf-idx-md5sum-files AND/OR --tarballs or --tarball-md5sum-files
+     [--vcfs <sample-level_vcf_file_path_comma_sep_if_multiple>]
+     [--vcf-md5sum-files <file_with_vcf_md5sum_comma_sep_same_order_as_vcfs>]
+     [--vcf-idxs <sample-level_vcf_idx_file_path_comma_sep_if_multiple>]
+     [--vcf-idx-md5sum-files <file_with_vcf_idx_md5sum_comma_sep_same_order_as_vcfs>]
+     # and/or
+     [--tarballs <tar.gz_non-vcf_files_comma_sep_if_multiple>]
+     [--tarball-md5sum-files <file_with_tarball_md5sum_comma_sep_same_order_as_tarball>]
+     # these are optional but highly recommended
+     [--workflow-src-url <http://... the source repo>]
+     [--workflow-url <http://... the packaged SeqWare Zip>]
+     [--workflow-name <workflow_name>]
+     [--workflow-version <workflow_version>]
+     [--vm-instance-type <vmInstanceType>]
+     [--vm-instance-cores <vmInstanceCores>]
+     [--vm-instance-mem-gb <vmInstanceMemGb>]
+     [--vm-location-code <vmLocationCode>]
+     # these are optional but used to link two or more distinct GNOS uploads for a given workflow (typically a workflow does a single upload to GNOS at the end but some divide the upload into multiple GNOS submissions)
+     [--workflow-file-subset <name_that_describes_this_subset_of_files_from_the_workflow_chosen_by_workflow_author>]
+     [--related-file-subset-uuids <comma_delimited_list_of_GNOS_analysis_uuids_of_the_other_uploads_related_to_this_upload_used_when_a_workflow_performs_multiple_gnos_uploads_and_wants_to_related_them_explicitly>]
+     # these are optional but required if using local file mode and not GNOS for metadata
+     [--metadata-paths <local_paths_for_specimen-level_aligned_BAM_xml_comma_sep> ]
+     # the rest are optional
+     [--timeout-min <20>]
+     [--retries <3>]
+     [--seqware-version <seqware_version_workflow_compiled_with>]
+     [--description-file <file_path_for_description_txt>]
+     [--study-refname-override <study_refname_override>]
+     [--center-override <center_override>]
+     [--ref-center-override <center_override>]
+     [--analysis-center-override <analysis_center_override>]
+     [--pipeline-json <pipeline_json_file>]
+     [--qc-metrics-json <qc_metrics_json_file>]
+     [--timing-metrics-json <timing_metrics_json_file>]
+     [--make-runxml]
+     [--make-expxml]
+     [--force-copy]
+     [--skip-validate]
+     [--skip-upload]
+     [--upload-archive <path_of_dir_to_copy_upload_to_and_make_tarball_uuid.tar.gz>]
+     [--uuid <uuis_for_use_as_upload_analysis_id>]
+     [--test]
 
 An example for the files that have been checked in along with this code:
 

gnos_upload_vcf.pl

@@ -188,6 +188,7 @@
 die "VCF and VCF index count don't match!\n"              if ( scalar(@vcf_arr) != scalar(@vcfs_idx_arr) );
 die "VCF index and VCF index md5sum count don't match!\n" if ( scalar(@vcf_arr) != scalar(@md5_idx_file_arr) );
 die "Tarball and Tarball md5sum count don't match!\n"     if ( scalar(@tarball_arr) != scalar(@md5_tarball_file_arr) );
+die "Keyfile $key not found!\n"                           if (!-e $key);
 
 say 'COPYING FILES TO OUTPUT DIR';
 my $link_method = ($force_copy)? 'rsync -rauv': 'ln -s';