From afee9526a463cfedca44cc55fd3deaf2473561f3 Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Mon, 5 Feb 2024 22:46:12 +0100
Subject: [PATCH] add test data

---
 src/lofreq/call/config.vsh.yaml            |  10 ++++++++++
 src/lofreq/call/test.sh                    |   0
 src/lofreq/call/test_data/a.bai            | Bin 0 -> 48 bytes
 src/lofreq/call/test_data/a.bam            | Bin 0 -> 352 bytes
 src/lofreq/call/test_data/genome.fasta     |   8 ++++++++
 src/lofreq/call/test_data/genome.fasta.fai |   4 ++++
 6 files changed, 22 insertions(+)
 create mode 100644 src/lofreq/call/test.sh
 create mode 100644 src/lofreq/call/test_data/a.bai
 create mode 100644 src/lofreq/call/test_data/a.bam
 create mode 100644 src/lofreq/call/test_data/genome.fasta
 create mode 100644 src/lofreq/call/test_data/genome.fasta.fai

diff --git a/src/lofreq/call/config.vsh.yaml b/src/lofreq/call/config.vsh.yaml
index d979c2b5..726e048a 100644
--- a/src/lofreq/call/config.vsh.yaml
+++ b/src/lofreq/call/config.vsh.yaml
@@ -25,6 +25,12 @@ functionality:
             Input BAM file.
           required: true
           example: "normal.bam"
+        - name: --input_bai
+          type: file
+          description: |
+            Index file for the input BAM file.
+          required: true
+          example: "normal.bai"
         - name: --ref
           alternatives: -f
           type: file
@@ -225,6 +231,10 @@ functionality:
   resources:
     - type: bash_script
       path: script.sh
+  test_resources:
+    - type: bash_script
+      path: test.sh
+    - path: test_data
 platforms:
   - type: docker
     image: quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10
diff --git a/src/lofreq/call/test.sh b/src/lofreq/call/test.sh
new file mode 100644
index 00000000..e69de29b
diff --git a/src/lofreq/call/test_data/a.bai b/src/lofreq/call/test_data/a.bai
new file mode 100644
index 0000000000000000000000000000000000000000..fd401327b0a9780b8f7ffbe9b4adb8d57f48407b
GIT binary patch
literal 48
RcmZ>A^kigVAPm@`N&qIR0N4Nk

literal 0
HcmV?d00001

diff --git a/src/lofreq/call/test_data/a.bam b/src/lofreq/call/test_data/a.bam
new file mode 100644
index 0000000000000000000000000000000000000000..109b5faccdff138c776f7d96a8bf2eb551d0c2d9
GIT binary patch
literal 352
zcmb2|=3rp}f&Xj_PR>jWj~GfPoaQ=YAmFOJ!(iRthKAQ^lO8c|y0lH9N!RP(-z&?s
zzBT3^xNja7yP~vE^4(lxV}pA}Z+fd+bRNm}DvQqlVtHKkuFEOW!~GXtbNyXsP|<!{
zG?ra!r{Z0=+?(!RA1tQ_FP~PVv|@jt%%o!0ZJe!o2VNXw$oJaw;t&^K=u9OQr;eOw
z=X9g&0@4DXwVW~Z*>t=jE_Lg^LyVvQ>{N1XF1V5!nlUdidBWeAm8Q#h6{hPJ{N>-_
zpKwFHg=bBiz0zX-_qCP(PqVMx&-~EQ>0dr01A{!87ZVtaQxg(?@U!~x$T{)w?BjXk
zk>sG(tk^uEJBgW@#e&V+*o9%EX4|ni9jUn;7dtW+3pP(+k2I4Kd>-N>-P<TN^~A=D
X60>_5`Zgqg3&Uc8Gy^j@NI?VuE3}7c

literal 0
HcmV?d00001

diff --git a/src/lofreq/call/test_data/genome.fasta b/src/lofreq/call/test_data/genome.fasta
new file mode 100644
index 00000000..e2015391
--- /dev/null
+++ b/src/lofreq/call/test_data/genome.fasta
@@ -0,0 +1,8 @@
+>SheilaA
+GCTAGCTCAGAAAAAAAAAA
+>SheilaB
+GCTAGCTCAGAAAAAAAAAA
+>SheilaC
+GCTAGCTCAGAAAAAAAAAA
+>SheilaD
+GCTAGCTCAGAAAAAAAAAA
diff --git a/src/lofreq/call/test_data/genome.fasta.fai b/src/lofreq/call/test_data/genome.fasta.fai
new file mode 100644
index 00000000..e42bfe2c
--- /dev/null
+++ b/src/lofreq/call/test_data/genome.fasta.fai
@@ -0,0 +1,4 @@
+SheilaA	20	9	20	21
+SheilaB	20	39	20	21
+SheilaC	20	69	20	21
+SheilaD	20	99	20	21