Merge pull request #60 from poseidon-framework/ssf_update

Changes for Poseidon v2.7.1

Author: nevrome

.github/workflows/mastodon.yml

@@ -0,0 +1,23 @@
+# https://github.com/marketplace/actions/fediverse-action
+
+name: toot-release
+
+# More triggers
+# https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#release
+#on: [push]
+on:
+  release:
+    types: [published]
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "ecoevo.social" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          # repo name can be queried with ${{ github.event.repository.name }}
+          message: "New Poseidon schema release ${{ github.event.release.tag_name }}! Please see the changelog here: https://poseidon-framework.github.io/#/changelog. New software versions are available to work with this new release: https://poseidon-framework.github.io/#/version_table #aDNA #OpenData"

README.md

@@ -154,7 +154,9 @@ Example:
 
 ## The `.ssf` file
 
-Poseidon 2.7.0 added an option to specify sequencing source data. This is a tab-separated table, much like the `.janno` file, but following a different schema, specified in the file `ssf_columns.tsv`.
+The `.ssf` file stores sequencing source data, so metainformation about the raw sequencing data behind the genotypes in a Poseidon package. The primary entities in this table are sequencing entities, typically corresponding to DNA libraries or even multiple runs/lanes of the same library.
 
-Note that the primary entities in this table are sequencing entities (typically corresponding to DNA libraries or even multiple runs/lanes of the same library). The link to the Individuals listed in the `.janno`-file are made through a foreign-key relationship into `Poseidon_ID`.
+It is a tab-separated table, much like the `.janno` file, but following a different schema, specified in the file `ssf_columns.tsv`. All columns of this schema are optional.
+
+The link to the individuals listed in the `.janno`-file (and therefore to the entire Poseidon package) is made through a many-to-many foreign-key relationship between the .janno column `Poseidon_ID` and the .ssf column `poseidon_IDs`. That means each entry in the .janno file can be linked to many rows in the .ssf file and vice versa.
 

ssf_columns.tsv

@@ -1,19 +1,19 @@
 sequencingSourceFile_column_name	description	data_type	multi	choice	range	choice_options	range_lower	range_upper	mandatory	unique
-poseidon_IDs	The Poseidon_IDs this sequencing entity corresponds to, from the Janno-file, multiple entries separated by ;	String	TRUE	FALSE	FALSE				TRUE	FALSE
-udg	UDG treatment	String	FALSE	TRUE	FALSE	minus;half;plus			FALSE	FALSE
-library_built	strandedness	String	FALSE	TRUE	FALSE	ds;ss			FALSE	FALSE
-sample_accession	The sample accession code as used in INSDC databases, including ENA and SRA (Example: SAMEA7050454)	String	FALSE	FALSE	FALSE				TRUE	TRUE
+poseidon_IDs	The Poseidon_IDs this sequencing entity corresponds to, from the Janno-file, multiple entries separated by ;	String	TRUE	FALSE	FALSE				FALSE	FALSE
+udg	The kind of UDG treatment applied to the library for this sequencing entity	String	FALSE	TRUE	FALSE	minus;half;plus			FALSE	FALSE
+library_built	The library preparation method applied for this sequencing entity (single- or double-stranded)	String	FALSE	TRUE	FALSE	ds;ss			FALSE	FALSE
+sample_accession	The sample accession code as used in INSDC databases, including ENA and SRA (Example: SAMEA7050454)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 study_accession	The study accession code as used in INSDC databases, including ENA and SRA (Example: PRJEB39316)	String	FALSE	FALSE	FALSE				FALSE	FALSE
-run_accession	The run accession code as used in INSDC databases, including ENA and SRA (Example: ERR4331996)	String	FALSE	FALSE	FALSE				FALSE	FALSE
+run_accession	The run accession code as used in INSDC databases, including ENA and SRA (Example: ERR4331996). This should be a unique identifier in most cases	String	FALSE	FALSE	FALSE				FALSE	FALSE
 sample_alias	The sample alias defined by the submitter	String	FALSE	FALSE	FALSE				FALSE	FALSE
-secondary_sample_accession	A secondary sample accession, as used at the ENA for historical reasons (Example: ERS4811084)	String	FALSE	FALSE	FALSE				FALSE	TRUE
+secondary_sample_accession	A secondary sample accession, as used at the ENA for historical reasons (Example: ERS4811084)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 first_public	The date (YYYY-MM-DD) this sample was first made public	Date	FALSE	FALSE	FALSE				FALSE	FALSE
 last_updated	The date (YYYY-MM-DD) this sample was last updated	Date	FALSE	FALSE	FALSE				FALSE	FALSE
 instrument_model	The name of the instrument used (Example: Illumina HiSeq 2500)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 library_layout	The library layout of the sequencing entity (Example: SINGLE)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 library_source	The source of the DNA library (Example: GENOMIC)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 instrument_platform	The platform brand or type of the sequencer (Example: ILLUMINA)	String	FALSE	FALSE	FALSE				FALSE	FALSE
-library_name	This is the library name the submitter has entered. Can sometimes be useful to figure out which Poseidon_ID this entity belongs to	String	FALSE	FALSE	FALSE				FALSE	FALSE
+library_name	The ID of the library. Defaults to the library name the submitter has entered to the raw sequencing data repository. Data entries across which optical duplicates could exist should have matching library names. Can sometimes be useful to figure out which Poseidon_ID this entity belongs to.	String	FALSE	FALSE	FALSE				FALSE	FALSE
 library_strategy	The strategy used to create the library (Example: WGS)	String	FALSE	FALSE	FALSE				FALSE	FALSE
 fastq_ftp	The FTP-link(s) (URL) to the FASTQ file(s) (Example: ftp.sra.ebi.ac.uk/vol1/fastq/ERR433/009/ERR4332639/ERR4332639.fastq.gz)	URL	TRUE	FALSE	FALSE				FALSE	FALSE
 fastq_aspera	The Aspera-link (URL) to the FASTQ-file(s). (Example: fasp.sra.ebi.ac.uk:/vol1/fastq/ERR433/009/ERR4332639/ERR4332639.fastq.gz)	URL	TRUE	FALSE	FALSE				FALSE	FALSE