From 8b708fbefd4d5a489c6d99af3fc23737a4be436e Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 30 May 2024 08:50:58 +0100
Subject: [PATCH] change script resource to samtools_fastq script, with dummy
 argument to specify the command

---
 src/samtools/samtools_fasta/config.vsh.yaml |  7 +++-
 src/samtools/samtools_fasta/script.sh       | 40 ---------------------
 2 files changed, 6 insertions(+), 41 deletions(-)
 delete mode 100644 src/samtools/samtools_fasta/script.sh

diff --git a/src/samtools/samtools_fasta/config.vsh.yaml b/src/samtools/samtools_fasta/config.vsh.yaml
index e5651789..46cccb0b 100644
--- a/src/samtools/samtools_fasta/config.vsh.yaml
+++ b/src/samtools/samtools_fasta/config.vsh.yaml
@@ -26,6 +26,11 @@ argument_groups:
         direction: output
   - name: Options
     arguments:
+      - name: --command
+        type: string
+        description: |
+          This is a dummy argument to use the same script for multiple samtools commands.
+        default: fasta
       - name: --no_suffix
         alternatives: -n
         type: boolean_true
@@ -170,7 +175,7 @@ argument_groups:
 
 resources:
   - type: bash_script
-    path: script.sh
+    path: ../samtools_fasta/script.sh
 test_resources:
   - type: bash_script
     path: test.sh
diff --git a/src/samtools/samtools_fasta/script.sh b/src/samtools/samtools_fasta/script.sh
deleted file mode 100644
index a3eb50e6..00000000
--- a/src/samtools/samtools_fasta/script.sh
+++ /dev/null
@@ -1,40 +0,0 @@
-#!/bin/bash
-
-## VIASH START
-## VIASH END
-
-set -e
-
-[[ "$par_no_suffix" == "false" ]] && unset par_no_suffix
-[[ "$par_suffix" == "false" ]] && unset par_suffix
-[[ "$par_use_oq" == "false" ]] && unset par_use_oq
-[[ "$par_copy_tags" == "false" ]] && unset par_copy_tags
-[[ "$par_casava" == "false" ]] && unset par_casava
-
-samtools fasta \
-    ${par_no_suffix:+-n} \
-    ${par_suffix:+-N} \
-    ${par_use_oq:+-O} \
-    ${par_singleton:+-s "$par_singleton"} \
-    ${par_copy_tags:+-t} \
-    ${par_copy_tags_list:+-T "$par_copy_tags_list"} \
-    ${par_read1:+-1 "$par_read1"} \
-    ${par_read2:+-2 "$par_read2"} \
-    ${par_output_reads:+-o "$par_output_reads"} \
-    ${par_output_reads_both:+-0 "$par_output_reads_both"} \
-    ${par_filter_flags:+-f "$par_filter_flags"} \
-    ${par_excl_flags:+-F "$par_excl_flags"} \
-    ${par_incl_flags:+--rf "$par_incl_flags"} \
-    ${par_excl_flags_all:+-G "$par_excl_flags_all"} \
-    ${par_aux_tag:+-d "$par_aux_tag"} \
-    ${par_aux_tag_file:+-D "$par_aux_tag_file"} \
-    ${par_casava:+-i} \
-    ${par_compression:+-c "$par_compression"} \
-    ${par_index1:+--i1 "$par_index1"} \
-    ${par_index2:+--i2 "$par_index2"} \
-    ${par_barcode_tag:+--barcode-tag "$par_barcode_tag"} \
-    ${par_quality_tag:+--quality-tag "$par_quality_tag"} \
-    ${par_index_format:+--index-format "$par_index_format"} \
-    "$par_input" \
-    > "$par_output"
-