rename component

viash-hub · Feb 26, 2024 · 21bd6a1 · 21bd6a1
1 parent 49d8d08
commit 21bd6a1
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Showing 7 changed files with 18 additions and 16 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,8 @@
 
 * `lofreq/indelqual`: Insert indel qualities into BAM file (PR #17).
 
+* `star/star_align_reads`: Align reads to a reference genome (PR #22).
+
 ## MAJOR CHANGES
 
 ## MINOR CHANGES

diff --git a/src/star/star_align/argument_groups.yaml → ...tar/star_align_reads/argument_groups.yaml b/src/star/star_align/argument_groups.yaml → ...tar/star_align_reads/argument_groups.yaml
diff --git a/src/star/star_align/config.vsh.yaml → src/star/star_align_reads/config.vsh.yaml b/src/star/star_align/config.vsh.yaml → src/star/star_align_reads/config.vsh.yaml
@@ -1,4 +1,4 @@
-name: star_align
+name: star_align_reads
 namespace: star
 description: |
   Aligns reads to a reference genome using STAR.

diff --git a/src/star/star_align/help.txt → src/star/star_align_reads/help.txt b/src/star/star_align/help.txt → src/star/star_align_reads/help.txt
diff --git a/src/star/star_align/script.py → src/star/star_align_reads/script.py b/src/star/star_align/script.py → src/star/star_align_reads/script.py
@@ -6,14 +6,14 @@
 ## VIASH START
 par = {
     "input": [
-        "src/star/star_align/test_data/a_R1.1.fastq",
-        "src/star/star_align/test_data/a_R1.2.fastq",
+        "src/star/star_align_reads/test_data/a_R1.1.fastq",
+        "src/star/star_align_reads/test_data/a_R1.2.fastq",
     ],
     "input_r2": [
-        "src/star/star_align/test_data/a_R2.1.fastq",
-        "src/star/star_align/test_data/a_R2.2.fastq",
+        "src/star/star_align_reads/test_data/a_R2.1.fastq",
+        "src/star/star_align_reads/test_data/a_R2.2.fastq",
     ],
-    "genomeDir": "src/star/star_align/test_data/genome.fasta",
+    "genomeDir": "src/star/star_align_reads/test_data/genome.fasta",
     "aligned_reads": "aligned_reads.sam"
 }
 meta = {

diff --git a/src/star/star_align/test.sh → src/star/star_align_reads/test.sh b/src/star/star_align/test.sh → src/star/star_align_reads/test.sh
@@ -3,8 +3,8 @@
 set -e
 
 ## VIASH START
-meta_executable="target/docker/star/star_align/star_align"
-meta_resources_dir="src/star/star_align"
+meta_executable="target/docker/star/star_align_reads/star_align_reads"
+meta_resources_dir="src/star/star_align_reads"
 ## VIASH END
 
 #########################################################################################
@@ -83,10 +83,10 @@ STAR \
 
 #########################################################################################
 
-mkdir star_align_se
-cd star_align_se
+mkdir star_align_reads_se
+cd star_align_reads_se
 
-echo "> Run star_align on SE"
+echo "> Run star_align_reads on SE"
 "$meta_executable" \
   --input "../reads_R1.fastq" \
   --genomeDir "../index/" \
@@ -134,10 +134,10 @@ cd ..
 
 #########################################################################################
 
-mkdir star_align_pe_minimal
-cd star_align_pe_minimal
+mkdir star_align_reads_pe_minimal
+cd star_align_reads_pe_minimal
 
-echo ">> Run star_align on PE"
+echo ">> Run star_align_reads on PE"
 "$meta_executable" \
   --input ../reads_R1.fastq \
   --input_r2 ../reads_R2.fastq \

diff --git a/src/star/star_align/utils/process_params.R → ...r/star_align_reads/utils/process_params.R b/src/star/star_align/utils/process_params.R → ...r/star_align_reads/utils/process_params.R
@@ -3,8 +3,8 @@ library(tidyverse)
 # This script processes the STAR aligner's help file
 # to create a viash argument_groups.yaml file.
 
-local_file <- "src/star/star_align/help.txt"
-yaml_file <- "src/star/star_align/argument_groups.yaml"
+local_file <- "src/star/star_align_reads/help.txt"
+yaml_file <- "src/star/star_align_reads/argument_groups.yaml"
 
 param_txt <- readr::read_lines(local_file)