diff --git a/.gitignore b/.gitignore index 0cd7483..4fa9229 100644 --- 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 new file mode 100644 index 0000000..fab96f0 --- /dev/null +++ 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" \ No newline at end of file diff --git a/.test/config/samples.csv b/.test/config/samples.csv new file mode 100644 index 0000000..04c3755 --- /dev/null +++ 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 \ No newline at end of file