fix: adding test-configuration

tdayris · Nov 22, 2023 · 7f26666 · 7f26666
1 parent be0319d
commit 7f26666
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Showing 3 changed files with 16 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,3 @@
-.test/config
 .test/linter.txt
 .test/format.txt
 .test/pipeline.txt

diff --git a/.test/config/config.yaml b/.test/config/config.yaml
@@ -0,0 +1,14 @@
+samples: config/samples.csv
+
+# # Optional parameters
+# params:
+#   bowtie2:
+#     # Optional parameters for bowtie2-build
+#     build: ""
+#     # Optional parameters for bowtie2-align
+#     align: ""
+#   sambamba:
+#     # Optional parameters for sambamba view
+#     view: "--format 'bam' --filter 'mapping_quality >= 30 and not (unmapped or mate_is_unmapped)' "
+#     # Optional parameters for sambamba markdup
+#     markdup: "--remove-duplicates"
diff --git a/.test/config/samples.csv b/.test/config/samples.csv
@@ -0,0 +1,2 @@
+sample_id,upstream_file,downstream_file,species,build,release
+sac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110