Reformatting and additions to meet workflow standards (#33)

* Minor changes *added model field in config to easier include other factor than condition *updated star to newest wrapper *added genome field in config if star index has to be build from scratch *formatted deseq2 output towards tsv *added normcount-table to deseq2 outputs *added option for metainformation to be appended to the count tables(e.g. gene symbols)

* Update

* Update

* Changed all output to results + updated schemas

* Fixed errors of reformat, included strandedness

* Added strandedness to units-tsv

* Added strandedness to units schema

* Made trimming optional

* Fixed error in config schema

* Added features for snakemake-workflows-catalog

* Fix

* Update config.yaml

* Update common.smk

* updated logging

* Github actions

* Changed sample column name

* Linting

* fmt

* fmt

* fmt

* test data

* test data

* test data2

* snakefmt

* fmt comments

* test data scerevisiae

* Fix Errors

* added new fq data

* Update deseq2 env

Co-authored-by: jafors <[email protected]>

.github/workflows/main.yml

@@ -0,0 +1,56 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches_ignore: []
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Checkout submodules
+      uses: textbook/[email protected]
+    - name: Formatting
+      uses: github/super-linter@v3
+      env:
+        VALIDATE_ALL_CODEBASE: false
+        DEFAULT_BRANCH: master
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        VALIDATE_SNAKEMAKE_SNAKEFMT: true
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: Linting
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--lint"
+
+  run-workflow:
+    runs-on: ubuntu-latest
+    needs:
+      - linting
+      - formatting
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v1
+    - name: Checkout submodules
+      uses: textbook/[email protected]
+    - name: Test workflow
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
+    - name: Test report
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--report report.zip"

.test/config/config.yaml

@@ -0,0 +1,41 @@
+# path or URL to sample sheet (TSV format, columns: sample, condition, ...)
+samples: config/samples.tsv
+# path or URL to sequencing unit sheet (TSV format, columns: sample, unit, fq1, fq2)
+# Units are technical replicates (e.g. lanes, or resequencing of the same biological
+# sample).
+units: config/units.tsv
+
+
+ref:
+  # Ensembl species name
+  species: saccharomyces_cerevisiae
+  # Ensembl release
+  release: 100
+  # Genome build
+  build: R64-1-1
+
+
+trimming:
+  activate: False
+
+mergeReads:
+  activate: False
+
+pca:
+  activate: True
+  labels:
+    # columns of sample sheet to use for PCA
+    - condition
+
+diffexp:
+  # contrasts for the deseq2 results method
+  contrasts:
+    treated-vs-untreated:
+      - treated
+      - untreated
+  model: ~condition
+
+params:
+  cutadapt-pe: ""
+  cutadapt-se: ""
+  star: "--outSAMtype BAM Unsorted"

.test/config/samples.tsv

@@ -0,0 +1,5 @@
+sample_name	condition
+A	treated
+B	untreated
+A2	treated
+B2	untreated

.test/config/units.tsv

@@ -0,0 +1,5 @@
+sample_name	unit_name	fq1	fq2	sra	adapters	strandedness
+A1	1	ngs-test-data/reads/a.scerevisiae.1.fq	ngs-test-data/reads/a.scerevisiae.2.fq			
+B1	1	ngs-test-data/reads/c.scerevisiae.1.fq	ngs-test-data/reads/c.scerevisiae.2.fq			
+A2	1	ngs-test-data/reads/a.scerevisiae.1.fq	ngs-test-data/reads/a.scerevisiae.2.fq			
+B2	1	ngs-test-data/reads/c.scerevisiae.1.fq	ngs-test-data/reads/c.scerevisiae.2.fq