Fix: #244 Nanopore readset file reference added

c3g · Jan 14, 2024 · 12df0a0 · 12df0a0
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diff --git a/docs/source/user_guide/pipelines/example_runs/nanopore-readset.inc b/docs/source/user_guide/pipelines/example_runs/nanopore-readset.inc
@@ -0,0 +1,30 @@
+.. note:: Nanopore Readset Format
+
+          Use the following **readset** file format for Nanopore, Nanopore CoV-Seq pipelines:
+
+          * Sample: must contain letters A-Z, numbers 0-9, hyphens (-) or underscores (_) only; mandatory;
+          * Readset: a unique readset name with the same allowed characters as above; mandatory;
+          * Run: a unique ONT run name, usually has a structure similar to PAE0000_a1b2c3d;
+          * Flowcell: code of the type of flowcell used, for example: the code for PromethION Flow Cell (R9.4) is FLO-PRO002;
+          * Library: code of the type of library preparation kit used, for example: the code for the Ligation Sequencing Kit is SQK-LSK109;
+          * Summary: path to the sequencing_summary.txt file outputted by the ONT basecaller; mandatory;
+          * FASTQ: mandatory, path to the fastq_pass directory, that is usually created by the basecaller
+          * FAST5: path to the directory containing the raw fast5 files, before basecalling
+
+          Example:
+
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+
+          |Sample  | Readset  | Run              | Flowcell        | Library     | Summary                                | FASTQ                       | FAST5                       |
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+
+          |sampleA | readset1 | PAE00001_abcd123 | FLO-PRO002      | SQK-LSK109  |path/to/readset1_sequencing_summary.txt | path/to/readset1/fastq_pass | path/to/readset1/fast5_pass |
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+          
+          |sampleA |readset2  | PAE00002_abcd456 | FLO-PRO002      | SQK-LSK109  |path/to/readset2_sequencing_summary.txt | path/to/readset2/fastq_pass | path/to/readset2/fast5_pass |
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+
+          |sampleA |readset3  | PAE00003_abcd789 | FLO-PRO002      | SQK-LSK109  |path/to/readset3_sequencing_summary.txt | path/to/readset3/fastq_pass | path/to/readset3/fast5_pass | 
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+
+          |sampleA |readset4  | PAE00004_abcd246 | FLO-PRO002      | SQK-LSK109  |path/to/readset4_sequencing_summary.txt | path/to/readset4/fastq_pass | path/to/readset4/fast5_pass |
+          +--------+----------+------------------+-----------------+-------------+----------------------------------------+-----------------------------+-----------------------------+
+
+
+
+
diff --git a/docs/source/user_guide/pipelines/gp_nanopore.rst b/docs/source/user_guide/pipelines/gp_nanopore.rst
@@ -84,7 +84,9 @@ Use the following commands to execute Nanopore Sequencing Pipeline:
 
 .. include:: /user_guide/pipelines/notes/scriptfile_deprecation.inc
 
-You can download the test dataset for this pipeline :ref:`here<docs_testdatasets>`. Nanopore pipeline readset file structure and format details are available `here <https://bitbucket.org/mugqic/genpipes/src/master/README.md#markdown-header-nanopore-pipeline>`_.
+.. include::  /user_guide/pipelines/example_runs/nanopore-readset.inc
+
+You can download the test dataset for this pipeline :ref:`here<docs_testdatasets>`. 
 
 ----
 

diff --git a/docs/source/user_guide/pipelines/gp_nanopore_covseq.rst b/docs/source/user_guide/pipelines/gp_nanopore_covseq.rst
@@ -93,7 +93,9 @@ Use the following commands to execute Nanopore sequencing pipeline:
 
 .. include:: /user_guide/pipelines/notes/artic_version.inc
 
-You can download the test dataset for this pipeline :ref:`here<docs_testdatasets>`. Nanopore CoVSeQ readset file structure and content details are available `here <https://bitbucket.org/mugqic/genpipes/src/master/README.md#markdown-header-nanopore-nanopore-cov-seq>`_.
+.. include::  /user_guide/pipelines/example_runs/nanopore-readset.inc
+
+You can download the test dataset for this pipeline :ref:`here<docs_testdatasets>`.
 
 ----