Forgot to include samples sheet tests

README.md

@@ -8,7 +8,7 @@ Dekupl-run handles the first part of the [DE-kupl pipeline](https://github.com/T
 the production of contigs from differentially expressed k-mers.
 - [Usage](#usage)
 - [Installation](#installation)
-    - [Option1 : Use dekupl-run with conda](#option1--use-dekupl-run-with-conda)
+    - [Option 1 : Use dekupl-run with conda](#option-1--use-dekupl-run-with-conda)
     - [Option 2: Use dekupl-run with Docker](#option-2-use-dekupl-run-with-docker)
     - [Option 3: Use dekupl-run with singularity](#option-3-use-dekupl-run-with-singularity)
     - [Option 4: Build and run yourself (not recommended)](#option-4-build-and-run-yourself-not-recommended)
@@ -36,7 +36,7 @@ Dekupl-run is a pipeline built with Snakemake. It works with a [configuration fi
 
 We recommand tu use [conda](https://anaconda.org/) to install dekupl-run, but you can also use Docker, Singularity and manual installation.
 
-### Option1 : Use dekupl-run with conda
+### Option 1 : Use dekupl-run with conda
 
 - **Step 1: Install conda.** If you do not have a conda distribution installed, we recommend to install miniconda as follows. See [Miniconda website](https://conda.io/miniconda.html) for other installation instructions (ex. for OSX).
     ```

tests/config_samples_sheet.json

@@ -0,0 +1,28 @@
+{
+  "fastq_dir": "data",
+  "nb_threads": 8,
+  "kmer_length": 31,
+  "lib_type": "rf",
+  "output_dir":"DEkupl_result_samles_sheet",
+  "diff_method": "Ttest",
+  "chunk_size":1000000,
+  "r1_suffix": "_1.fastq.gz",
+  "r2_suffix": "_2.fastq.gz",
+  "transcript_fasta": "tests/gencode.v24.transcripts.head1000.transcriptNames.fa",
+  "transcript_to_gene": "tests/gencode.v24.transcripts.head1000.mapping.tsv",
+  "samples_tsv": "tests/samples.tsv",
+
+  "dekupl_counter": {
+    "min_recurrence": 2,
+    "min_recurrence_abundance": 5
+  },
+
+  "diff_analysis": {
+    "condition" : {
+      "A": "A",
+      "B": "B"
+    },
+    "pvalue_threshold": 0.2,
+    "log2fc_threshold": 0
+  }
+}

tests/samples.tsv

@@ -0,0 +1,5 @@
+name	condition
+sample1	A
+sample2	A
+sample3	B
+sample4	B