more consistent arg names, remove "paired" argument and adapt script

src/umi_tools/umi_tools_extract/config.vsh.yaml

@@ -28,6 +28,7 @@ argument_groups:
       description: File containing the input data for the R2 reads (if paired). If provided, a <list of other required arguments> need to be provided.
       example: sample_R2.fastq
     - name: --bc_pattern
+      alternatives: -p
       type: string
       description: |
         The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides 
@@ -38,7 +39,7 @@ argument_groups:
 
   - name: "Output"
     arguments:  
-    - name: --read1_out
+    - name: --output
       type: file
       required: true
       description: Output file for read 1.

src/umi_tools/umi_tools_extract/script.sh

@@ -7,7 +7,6 @@ set -exo pipefail
 
 test_dir="${metal_executable}/test_data"
 
-[[ "$par_paired" == "false" ]] && unset par_paired
 [[ "$par_error_correct_cell" == "false" ]] && unset par_error_correct_cell
 [[ "$par_reconcile_pairs" == "false" ]] && unset par_reconcile_pairs
 [[ "$par_three_prime" == "false" ]] && unset par_three_prime
@@ -19,29 +18,37 @@ test_dir="${metal_executable}/test_data"
 # Check if we have the correct number of input files and patterns for paired-end or single-end reads
 
 # For paired-end rends, check that we have two read files, two patterns
-if [ -n "$par_paired" ]; then
-    if [ -z "$par_input" ] || [ -z "$par_read2_in" ] ||
-       [ -z "$par_bc_pattern" ] || [ -z "$par_bc_pattern2" ]; 
-        then
-        echo "Paired end input requires two read files, two UMI patterns, and two output files"
+# Check for paired-end inputs
+if [ -n "$par_input" ] && [ -n "$par_read2_in" ]; then
+    # Paired-end checks: Ensure both UMI patterns are provided
+    if [ -z "$par_bc_pattern" ] || [ -z "$par_bc_pattern2" ]; then
+        echo "Paired end input requires two UMI patterns."
         exit 1
     fi
-else # For single-end reads, check that we have only one read file, one pattern
-    if [ -n "$par_read2_in" ] || [ -n "$par_bc_pattern2" ]; then
-        echo "Single end input requires only one read file and one UMI pattern"
+elif [ -n "$par_input" ]; then
+    # Single-end checks: Ensure no second read or UMI pattern for the second read is provided
+    if [ -n "$par_bc_pattern2" ]; then
+        echo "Single end input requires only one read file and one UMI pattern."
         exit 1
-    # if par_umi_discard_read is not empty or not 0:
-    elif [ -n "$par_umi_discard_read" ] && [ "$par_umi_discard_read" != 0 ]; then
+    fi
+    # Check that discard_read is not set or set to 0 for single-end reads
+    if [ -n "$par_umi_discard_read" ] && [ "$par_umi_discard_read" != 0 ]; then
         echo "umi_discard_read is only valid when processing paired end reads."
         exit 1
     fi
+else
+    # No inputs provided
+    echo "No input files provided."
+    exit 1
 fi
 
 
+
+
 umi_tools extract \
     -I "$par_input" \
     ${par_read2_in:+ --read2-in "$par_read2_in"} \
-    -S "$par_read1_out" \
+    -S "$par_output" \
     ${par_read2_out:+--read2-out "$par_read2_out"} \
     ${par_extract_method:+--extract-method "$par_extract_method"} \
     --bc-pattern "$par_bc_pattern" \

src/umi_tools/umi_tools_extract/test.sh

@@ -8,7 +8,6 @@ echo ">>> Testing $meta_functionality_name"
 
 echo ">>> Test 1: Testing for paired-end reads"
 "$meta_executable" \
-    --paired \
     --input "$test_dir/scrb_seq_fastq.1_30"\
     --read2_in "$test_dir/scrb_seq_fastq.2_30" \
     --bc_pattern "CCCCCCNNNNNNNNNN"\
@@ -17,7 +16,7 @@ echo ">>> Test 1: Testing for paired-end reads"
     --umi_separator '_' \
     --grouping_method directional \
     --umi_discard_read 0 \
-    --read1_out scrb_seq_fastq.1_30.extract \
+    --output scrb_seq_fastq.1_30.extract \
     --read2_out scrb_seq_fastq.2_30.extract \
     --random_seed 1
 
@@ -39,7 +38,6 @@ rm scrb_seq_fastq.1_30.extract scrb_seq_fastq.2_30.extract
 
 echo ">>> Test 2: Testing for paired-end reads with umi_discard_reads option"
 "$meta_executable" \
-    --paired \
     --input "$test_dir/scrb_seq_fastq.1_30" \
     --read2_in "$test_dir/scrb_seq_fastq.2_30" \
     --bc_pattern CCCCCCNNNNNNNNNN \
@@ -48,7 +46,7 @@ echo ">>> Test 2: Testing for paired-end reads with umi_discard_reads option"
     --umi_separator '_' \
     --grouping_method directional \
     --umi_discard_read 2 \
-    --read1_out scrb_seq_fastq.1_30.extract \
+    --output scrb_seq_fastq.1_30.extract \
     --random_seed 1
 
 echo ">> Checking if the correct files are present"
@@ -71,7 +69,7 @@ echo ">>> Test 3: Testing for single-end reads"
     --extract_method regex \
     --umi_separator '_' \
     --grouping_method directional \
-    --read1_out slim_30.extract \
+    --output slim_30.extract \
     --random_seed 1 
 
 echo ">> Checking if the correct files are present"