diff options
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.html | 6 | ||||
| -rw-r--r-- | doc/blog/using-covid-19-pubseq-part3.org | 6 | ||||
| -rw-r--r-- | example/esr_example.yaml | 1 | ||||
| -rw-r--r-- | example/maximum_metadata_example.yaml | 2 | ||||
| -rw-r--r-- | example/uthsc_example.yaml | 2 | ||||
| -rw-r--r-- | scripts/uthsc_samples/template.yaml | 1 | ||||
| -rw-r--r-- | test/data/input/TN_UT2.yaml | 1 |
7 files changed, 8 insertions, 11 deletions
diff --git a/doc/blog/using-covid-19-pubseq-part3.html b/doc/blog/using-covid-19-pubseq-part3.html index aea74ad..2651f85 100644 --- a/doc/blog/using-covid-19-pubseq-part3.html +++ b/doc/blog/using-covid-19-pubseq-part3.html @@ -358,8 +358,8 @@ the web form. Here we add some extra information. <p> This is a string field that defines a unique sample identifier by the submitter. In addition to sample_id we also have host_id, -provider_sample_id and submitter_sample_id where host is the host the -sample came from, provider sample is the institution sample id and +provider and submitter_sample_id where host is the host the +sample came from, provider sample is the institution id and submitter is the submitting individual id. host_id is important when multiple sequences come from the same host. Make sure not to have spaces in the sample_id. @@ -599,7 +599,7 @@ submitter: submitter_address: John Doe's address originating_lab: John Doe kitchen lab_address: John Doe's address - provider_sample_id: XXX<span style="color: #8bc34a;">1</span> + provider: XXX<span style="color: #8bc34a;">1</span> submitter_sample_id: XXX<span style="color: #8bc34a;">2</span> publication: PMID<span style="color: #8bc34a;">00001113</span> submitter_orcid: [https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>,https://orcid.org/<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0000</span>-<span style="color: #8bc34a;">0001</span>] diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org index 7336cf6..307a87a 100644 --- a/doc/blog/using-covid-19-pubseq-part3.org +++ b/doc/blog/using-covid-19-pubseq-part3.org @@ -83,8 +83,8 @@ the web form. Here we add some extra information. This is a string field that defines a unique sample identifier by the submitter. In addition to sample_id we also have host_id, -provider_sample_id and submitter_sample_id where host is the host the -sample came from, provider sample is the institution sample id and +provider and submitter_sample_id where host is the host the +sample came from, provider sample is the institution id and submitter is the submitting individual id. host_id is important when multiple sequences come from the same host. Make sure not to have spaces in the sample_id. @@ -245,7 +245,7 @@ a more elaborate example (note most fields are optional) may look like submitter_address: John Doe's address originating_lab: John Doe kitchen lab_address: John Doe's address - provider_sample_id: XXX1 + provider: XXX1 submitter_sample_id: XXX2 publication: PMID00001113 submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] diff --git a/example/esr_example.yaml b/example/esr_example.yaml index 693aff3..c97d0bf 100644 --- a/example/esr_example.yaml +++ b/example/esr_example.yaml @@ -33,7 +33,6 @@ submitter: submitter_name: [Joep de Ligt] submitter_address: "PO Box 50348, Porirua 5240, New Zealand" originating_lab: ESR - provider_sample_id: "20VR0174" submitter_sample_id: "PRJNA648792" submitted_to: https://www.ncbi.nlm.nih.gov/biosample publication: https://doi.org/10.1101/2020.08.05.20168930 diff --git a/example/maximum_metadata_example.yaml b/example/maximum_metadata_example.yaml index cd8890d..8bc08de 100644 --- a/example/maximum_metadata_example.yaml +++ b/example/maximum_metadata_example.yaml @@ -45,7 +45,7 @@ submitter: submitter_address: John Doe's address originating_lab: John Doe kitchen lab_address: John Doe's address - provider_sample_id: XXX1 + provider: XXX1 submitter_sample_id: XXX2 publication: PMID00001113 submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] diff --git a/example/uthsc_example.yaml b/example/uthsc_example.yaml index 2384114..661cf60 100644 --- a/example/uthsc_example.yaml +++ b/example/uthsc_example.yaml @@ -33,7 +33,7 @@ submitter: submitter_name: [Mariah Taylor] submitter_address: UTHSC, Memphis, Tennessee 38163, USA originating_lab: Regional Biocontainment Laboratory - provider_sample_id: XXX1 + provider: XXX1 submitter_sample_id: XXX2 publication: PMID00001113 submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001] diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml index dab8634..9f5efd2 100644 --- a/scripts/uthsc_samples/template.yaml +++ b/scripts/uthsc_samples/template.yaml @@ -31,6 +31,5 @@ submitter: submitter_name: [Mariah Taylor, Colleen B. Jonsson, Pjotr Prins] submitter_address: UTHSC, Memphis, Tennessee 38163, USA originating_lab: Regional Biocontainment Laboratory, Memphis, TN - provider_sample_id: $sample_id submitter_sample_id: $sample_id submitter_orcid: [https://orcid.org/0000-0002-2640-7672,https://orcid.org/0000-0002-8021-9162] diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml index f2f190b..55a7591 100644 --- a/test/data/input/TN_UT2.yaml +++ b/test/data/input/TN_UT2.yaml @@ -31,6 +31,5 @@ submitter: submitter_name: [Mariah Taylor, Colleen B. Jonsson, Pjotr Prins] submitter_address: UTHSC, Memphis, Tennessee 38163, USA originating_lab: Regional Biocontainment Laboratory, Memphis, TN - provider_sample_id: TN_UT2 submitter_sample_id: TN_UT2 submitter_orcid: [https://orcid.org/0000-0002-2640-7672,https://orcid.org/0000-0002-8021-9162] |