Build branch main with version main (d8c0c0f)

Build pipeline: viash-hub.htrnaseq.main-fc9g5

Source commit: d8c0c0f518

Source message: Create umi_length parameter and infer barcode length from sequence (#27)

target/executable/parallel_map/.config.vsh.yaml

@@ -68,14 +68,6 @@ argument_groups:
     multiple_sep: ";"
 - name: "Barcode arguments"
   arguments:
-  - type: "integer"
-    name: "--wellBarcodesLength"
-    description: "The length of the well barcodes"
-    info: null
-    required: true
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
   - type: "integer"
     name: "--umiLength"
     description: "The length of the UMIs"
@@ -264,8 +256,8 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"

target/executable/parallel_map/parallel_map

@@ -197,10 +197,6 @@ function ViashHelp {
   echo "        The barcodes/wells to process"
   echo ""
   echo "Barcode arguments:"
-  echo "    --wellBarcodesLength"
-  echo "        type: integer, required parameter"
-  echo "        The length of the well barcodes"
-  echo ""
   echo "    --umiLength"
   echo "        type: integer, required parameter"
   echo "        The length of the UMIs"
@@ -517,9 +513,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -721,17 +717,6 @@ while [[ $# -gt 0 ]]; do
             fi
             shift 1
             ;;
-        --wellBarcodesLength)
-            [ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WELLBARCODESLENGTH="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --wellBarcodesLength. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --wellBarcodesLength=*)
-            [ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength=*\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WELLBARCODESLENGTH=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
         --umiLength)
             [ -n "$VIASH_PAR_UMILENGTH" ] && ViashError Bad arguments for option \'--umiLength\': \'$VIASH_PAR_UMILENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_UMILENGTH="$2"
@@ -975,10 +960,6 @@ if [ -z ${VIASH_PAR_BARCODES+x} ]; then
   ViashError '--barcodes' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
 fi
-if [ -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then
-  ViashError '--wellBarcodesLength' is a required argument. Use "--help" to get more information on the parameters.
-  exit 1
-fi
 if [ -z ${VIASH_PAR_UMILENGTH+x} ]; then
   ViashError '--umiLength' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
@@ -1054,12 +1035,6 @@ if [ ! -z "$VIASH_PAR_GENOMEDIR" ] && [ ! -e "$VIASH_PAR_GENOMEDIR" ]; then
 fi
 
 # check whether parameters values are of the right type
-if [[ -n "$VIASH_PAR_WELLBARCODESLENGTH" ]]; then
-  if ! [[ "$VIASH_PAR_WELLBARCODESLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
-    ViashError '--wellBarcodesLength' has to be an integer. Use "--help" to get more information on the parameters.
-    exit 1
-  fi
-fi
 if [[ -n "$VIASH_PAR_UMILENGTH" ]]; then
   if ! [[ "$VIASH_PAR_UMILENGTH" =~ ^[-+]?[0-9]+$ ]]; then
     ViashError '--umiLength' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1289,7 +1264,6 @@ $( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed
 $( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
 $( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
 $( if [ ! -z ${VIASH_PAR_BARCODES+x} ]; then echo "${VIASH_PAR_BARCODES}" | sed "s#'#'\"'\"'#g;s#.*#par_barcodes='&'#" ; else echo "# par_barcodes="; fi )
-$( if [ ! -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then echo "${VIASH_PAR_WELLBARCODESLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_wellBarcodesLength='&'#" ; else echo "# par_wellBarcodesLength="; fi )
 $( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
 $( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\"'\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
 $( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\"'\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
@@ -1376,16 +1350,17 @@ fi
 
 # Define the function that will be used to run a single job
 function _run() {
-  local par_wellBarcodeLength="\$1"
-  local par_UMIlength="\$2"
-  local par_output="\$3"
-  local par_genomeDir="\$4"
-  local par_limitBAMsortRAM="\$5"
-  local par_runThreadN="\$6"
-  local barcode="\$7"
-  local input_R1="\$8"
-  local input_R2="\$9"
-  local par_UMIstart=\$((\$par_wellBarcodeLength + 1))
+  local par_UMIlength="\$1"
+  local par_output="\$2"
+  local par_genomeDir="\$3"
+  local par_limitBAMsortRAM="\$4"
+  local par_runThreadN="\$5"
+  local barcode="\$6"
+  local input_R1="\$7"
+  local input_R2="\$8"
+
+  local barcode_length="\${#barcode}"
+  local umi_start="\$((\$barcode_length + 1))"
 
   set -eo pipefail
 
@@ -1481,8 +1456,8 @@ function _run() {
     --outSAMtype BAM SortedByCoordinate \\
     --soloCBstart 1 \\
     --readFilesType "Fastx" \\
-    --soloCBlen "\$par_wellBarcodeLength" \\
-    --soloUMIstart "\$par_UMIstart" \\
+    --soloCBlen "\$barcode_length" \\
+    --soloUMIstart "\$umi_start" \\
     --soloUMIlen "\$par_UMIlength" \\
     --soloBarcodeReadLength 0 \\
     --soloStrand Unstranded \\
@@ -1538,7 +1513,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
               "--joblog" "\$par_joblog" "_run" "{}")
 
 # Arguments for which there is one value, so these will not create extra jobs
-parallel_cmd+=(":::" "\$par_wellBarcodesLength" ":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
+parallel_cmd+=(":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
 
 # Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
 # Thus, these argument lists should have the same length.