fix: batch correction (#89)

* feat: providing ngs-test-data

* fix: deleted own old test data

* feat: allowing for batch correction

* feat: renaming 'batch_effect' to 'batch'

* fix: linter did not accout for latest changes

* feat: actual consideration of the batch effect in the DE script

* fix: attempting with a mini default profile#

* fix: test with workflow-profile flag

* fix: added missing unzip package to curl.env

* fix: typo

* fix: added missing design_factors

* fix: removed old test data

* fix: only considering one confounding variable during CI tests

* fix: renamed and added ncbi-datasets-cli as a package to env/reference.yml

* feat: replaced curl downloads wtih ncbi-datasets-cli download by accession number to avoid unstable URLs

* fix: corrected typos

* fix: untested - new data in test config

* fix: gnarf - formatting

.test/config-simple/samples.csv

@@ -1,3 +1,3 @@
 sample  condition   condition2	batch    platform    purity
-01  	male        condition2  batch1          NANOPORE    1
-02      female      condition2  batch1          NANOPORE    1
+../ngs-test-data/reads/a.chr21.1.fq  	treated        condition2  batch1          NANOPORE    1
+../ngs-test-data/reads/b.chr21.1.fq      untreated      condition2  batch1          NANOPORE    1

workflow/rules/ref.smk

@@ -1,6 +1,7 @@
 localrules:
     get_genome,
-    get_annotation,
+    extract_annotation,
+    extract_genome,
 
 
 rule get_genome:
@@ -40,7 +41,7 @@ rule extract_genome:
 
 rule extract_annotation:
     input:
-        rules.get_annotation.output,
+        rules.get_genome.output,
     output:
         "references/genomic.gff",
     group:
@@ -50,7 +51,7 @@ rule extract_annotation:
     log:
         "logs/refs/get_annotation.log",
     conda:
-        "../envs/references.yml"
+        "../envs/reference.yml"
     shell:
         """
         unzip -p {input} ncbi_dataset/data/{params.accession}/*.gff > references/genomic.gff 2> {log};