From ece2ffb6a6894fce8516e9cd4889d16f94c9b2ab Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Mon, 1 Apr 2024 16:55:08 +0100
Subject: [PATCH] Change component name, fix version.txt text

---
 .../{index => samtools_index}/config.vsh.yaml       |   9 +++++----
 src/samtools/{index => samtools_index}/help.txt     |   0
 src/samtools/{index => samtools_index}/script.sh    |   0
 src/samtools/{index => samtools_index}/test.sh      |   0
 .../test_data/a.sorted.bam                          | Bin
 .../test_data/a_4_ref.sorted.bam.bai                | Bin
 .../test_data/a_multiple_ref.sorted.bam.bai         | Bin
 .../test_data/a_ref.sorted.bam.bai                  | Bin
 .../test_data/a_ref.sorted.bam.csi                  | Bin
 .../{index => samtools_index}/test_data/script.sh   |   0
 10 files changed, 5 insertions(+), 4 deletions(-)
 rename src/samtools/{index => samtools_index}/config.vsh.yaml (85%)
 rename src/samtools/{index => samtools_index}/help.txt (100%)
 rename src/samtools/{index => samtools_index}/script.sh (100%)
 rename src/samtools/{index => samtools_index}/test.sh (100%)
 rename src/samtools/{index => samtools_index}/test_data/a.sorted.bam (100%)
 rename src/samtools/{index => samtools_index}/test_data/a_4_ref.sorted.bam.bai (100%)
 rename src/samtools/{index => samtools_index}/test_data/a_multiple_ref.sorted.bam.bai (100%)
 rename src/samtools/{index => samtools_index}/test_data/a_ref.sorted.bam.bai (100%)
 rename src/samtools/{index => samtools_index}/test_data/a_ref.sorted.bam.csi (100%)
 rename src/samtools/{index => samtools_index}/test_data/script.sh (100%)

diff --git a/src/samtools/index/config.vsh.yaml b/src/samtools/samtools_index/config.vsh.yaml
similarity index 85%
rename from src/samtools/index/config.vsh.yaml
rename to src/samtools/samtools_index/config.vsh.yaml
index 07d81728..da4cd76a 100644
--- a/src/samtools/index/config.vsh.yaml
+++ b/src/samtools/samtools_index/config.vsh.yaml
@@ -1,13 +1,13 @@
 name: samtools_index
 namespace: samtools
-description: Index SAM/BAM/CRAM files
+description: Index SAM/BAM/CRAM files.
 keywords: [index, bam, sam, cram]
 links:
   homepage: https://www.htslib.org/
   documentation: https://www.htslib.org/doc/samtools-index.html
-  repository: https://github.com/samtools/samtools.git
+  repository: https://github.com/samtools/samtools
 references: 
-  doi: 10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008
+  doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008]
 license: MIT/Expat
 
 argument_groups:
@@ -67,7 +67,8 @@ engines:
     setup:
       - type: docker
         run: |
-          echo "$(samtools --version 2>&1)" > /var/software_versions.txt
+        samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \
+        sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt
 runners:
 - type: executable
 - type: nextflow
\ No newline at end of file
diff --git a/src/samtools/index/help.txt b/src/samtools/samtools_index/help.txt
similarity index 100%
rename from src/samtools/index/help.txt
rename to src/samtools/samtools_index/help.txt
diff --git a/src/samtools/index/script.sh b/src/samtools/samtools_index/script.sh
similarity index 100%
rename from src/samtools/index/script.sh
rename to src/samtools/samtools_index/script.sh
diff --git a/src/samtools/index/test.sh b/src/samtools/samtools_index/test.sh
similarity index 100%
rename from src/samtools/index/test.sh
rename to src/samtools/samtools_index/test.sh
diff --git a/src/samtools/index/test_data/a.sorted.bam b/src/samtools/samtools_index/test_data/a.sorted.bam
similarity index 100%
rename from src/samtools/index/test_data/a.sorted.bam
rename to src/samtools/samtools_index/test_data/a.sorted.bam
diff --git a/src/samtools/index/test_data/a_4_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_4_ref.sorted.bam.bai
similarity index 100%
rename from src/samtools/index/test_data/a_4_ref.sorted.bam.bai
rename to src/samtools/samtools_index/test_data/a_4_ref.sorted.bam.bai
diff --git a/src/samtools/index/test_data/a_multiple_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_multiple_ref.sorted.bam.bai
similarity index 100%
rename from src/samtools/index/test_data/a_multiple_ref.sorted.bam.bai
rename to src/samtools/samtools_index/test_data/a_multiple_ref.sorted.bam.bai
diff --git a/src/samtools/index/test_data/a_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_ref.sorted.bam.bai
similarity index 100%
rename from src/samtools/index/test_data/a_ref.sorted.bam.bai
rename to src/samtools/samtools_index/test_data/a_ref.sorted.bam.bai
diff --git a/src/samtools/index/test_data/a_ref.sorted.bam.csi b/src/samtools/samtools_index/test_data/a_ref.sorted.bam.csi
similarity index 100%
rename from src/samtools/index/test_data/a_ref.sorted.bam.csi
rename to src/samtools/samtools_index/test_data/a_ref.sorted.bam.csi
diff --git a/src/samtools/index/test_data/script.sh b/src/samtools/samtools_index/test_data/script.sh
similarity index 100%
rename from src/samtools/index/test_data/script.sh
rename to src/samtools/samtools_index/test_data/script.sh