Revert "Merge branch 'viash-hub:main' into fix_configs"

This reverts commit 8324bd9, reversing changes made to 2f72500.
emmarousseau · Apr 13, 2024 · c7a8d72 · c7a8d72
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -38,9 +38,6 @@
 * `samtools`:
     - `samtools/flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
     - `samtools/idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
-    - `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
-    - `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
-    - `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
 
 ## MAJOR CHANGES
 

diff --git a/src/samtools/samtools_index/config.vsh.yaml b/src/samtools/samtools_index/config.vsh.yaml
diff --git a/src/samtools/samtools_index/help.txt b/src/samtools/samtools_index/help.txt
diff --git a/src/samtools/samtools_index/script.sh b/src/samtools/samtools_index/script.sh
diff --git a/src/samtools/samtools_index/test.sh b/src/samtools/samtools_index/test.sh
diff --git a/src/samtools/samtools_index/test_data/a.sorted.bam b/src/samtools/samtools_index/test_data/a.sorted.bam
diff --git a/src/samtools/samtools_index/test_data/a_4_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_4_ref.sorted.bam.bai
diff --git a/src/samtools/samtools_index/test_data/a_multiple_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_multiple_ref.sorted.bam.bai
diff --git a/src/samtools/samtools_index/test_data/a_ref.sorted.bam.bai b/src/samtools/samtools_index/test_data/a_ref.sorted.bam.bai
diff --git a/src/samtools/samtools_index/test_data/a_ref.sorted.bam.csi b/src/samtools/samtools_index/test_data/a_ref.sorted.bam.csi
diff --git a/src/samtools/samtools_index/test_data/script.sh b/src/samtools/samtools_index/test_data/script.sh
diff --git a/src/samtools/samtools_sort/config.vsh.yaml b/src/samtools/samtools_sort/config.vsh.yaml