diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..18156e9 --- /dev/null +++ b/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 diff --git a/README.md b/README.md index 738b345..064f7a7 100644 --- a/README.md +++ b/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 - --vcfs - --vcf-md5sum-files - --vcf-idxs - --vcf-idx-md5sum-files - --tarballs - --tarball-md5sum-files - --outdir - --key - --upload-url - [--workflow-src-url ] - [--workflow-url ] - [--workflow-name ] - [--workflow-version ] - [--seqware-version ] - [--description-file ] - [--study-refname-override ] - [--analysis-center-override ] - [--pipeline-json ] - [--qc-metrics-json ] - [--timing-metrics-json ] - [--make-runxml] - [--make-expxml] - [--force-copy] - [--skip-validate] - [--skip-upload] - [--test] + USAGE: 'perl gnos_upload_vcf.pl + --metadata-urls + --outdir + --key + --upload-url + # you must specify --vcfs, --vcf-md5sum-files, --vcf-idxs, and --vcf-idx-md5sum-files AND/OR --tarballs or --tarball-md5sum-files + [--vcfs ] + [--vcf-md5sum-files ] + [--vcf-idxs ] + [--vcf-idx-md5sum-files ] + # and/or + [--tarballs ] + [--tarball-md5sum-files ] + # these are optional but highly recommended + [--workflow-src-url ] + [--workflow-url ] + [--workflow-name ] + [--workflow-version ] + [--vm-instance-type ] + [--vm-instance-cores ] + [--vm-instance-mem-gb ] + [--vm-location-code ] + # 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 ] + [--related-file-subset-uuids ] + # these are optional but required if using local file mode and not GNOS for metadata + [--metadata-paths ] + # the rest are optional + [--timeout-min <20>] + [--retries <3>] + [--seqware-version ] + [--description-file ] + [--study-refname-override ] + [--center-override ] + [--ref-center-override ] + [--analysis-center-override ] + [--pipeline-json ] + [--qc-metrics-json ] + [--timing-metrics-json ] + [--make-runxml] + [--make-expxml] + [--force-copy] + [--skip-validate] + [--skip-upload] + [--upload-archive ] + [--uuid ] + [--test] An example for the files that have been checked in along with this code: diff --git a/gnos_upload_vcf.pl b/gnos_upload_vcf.pl index d2d1021..6b6d2d8 100644 --- a/gnos_upload_vcf.pl +++ b/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';