actual eager param

ktmeaton · Apr 23, 2020 · 7981226 · 7981226
1 parent 8edd221
commit 7981226
Showing 1 changed file with 21 additions and 0 deletions.
diff --git a/eager/README_EAGER.md b/eager/README_EAGER.md
@@ -20,6 +20,7 @@ git pull
 
 ## EAGER Run
 
+Basic Testing
 ```
 nextflow run nf-core/eager -r tsv-input \
   --tsv_input metadata/metadata_BronzeAge.tsv \
@@ -28,3 +29,23 @@ nextflow run nf-core/eager -r tsv-input \
   --max_memory '8.GB' \
   --max_cpus 8
 ```
+Actual parameter
+```
+nextflow run nf-core/eager -r tsv-input \
+  --tsv_input metadata/metadata_BronzeAge.tsv \
+  --outdir test \
+  --fasta reference/GCF_000009065.1_ASM906v1_genomic.fna \
+  --clip_readlength 35 \
+  --preserve5p \
+  --mergedonly \
+  --mapper bwaaln \
+  --bwaalnn 0.01 \
+  --bwaalnl 32 \
+  --bwaalnk 2 \
+  --bam_mapping_quality_threshold 30 \
+  --dedupper dedup \
+  --damageprofiler_length 35 \
+  --damageprofiler_yaxis 0.30 \
+  -resume 1da96824-731c-434a-a2c3-ef68f95572b1
+  --
+```