Build branch add-labels with version add-labels (59cbb30)

Build pipeline: viash-hub.rnaseq.add-labels-cdc96 Source commit: 59cbb30eec Source message: Fix config
2024-12-02 15:32:27 +00:00
parent 13477349f0
commit 5f8830f4c8
397 changed files with 36174 additions and 53686 deletions
--- a/target/executable/tximport/.config.vsh.yaml
+++ b/target/executable/tximport/.config.vsh.yaml
@@ -11,7 +11,7 @@ argument_groups:
    required: false
    direction: "input"
    multiple: true
-    multiple_sep: ","
+    multiple_sep: ";"
  - type: "file"
    name: "--tx2gene_tsv"
    info: null
@@ -82,7 +82,7 @@ argument_groups:
    name: "--lengths_gene"
    info: null
    default:
-    - "merged.gene_length.tsv"
+    - "merged.gene_lengths.tsv"
    must_exist: true
    create_parent: true
    required: false
@@ -115,7 +115,7 @@ argument_groups:
    name: "--lengths_transcript"
    info: null
    default:
-    - "merged.transcript_length.tsv"
+    - "merged.transcript_lengths.tsv"
    must_exist: true
    create_parent: true
    required: false
@@ -132,6 +132,10 @@ resources:
  path: "nextflow_labels.config"
  dest: "nextflow_labels.config"
 description: "Get dataframe linking transcript ID, gene ID, and gene name"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
 info:
  migration_info:
    git_repo: "https://github.com/nf-core/rnaseq.git"
@@ -145,7 +149,7 @@ requirements:
 repositories:
 - type: "vsh"
  name: "biobox"
-  repo: "vsh/biobox"
+  repo: "biobox"
  tag: "main"
 - type: "vsh"
  name: "craftbox"
@@ -158,9 +162,6 @@ runners:
 - type: "nextflow"
  id: "nextflow"
  directives:
-    label:
-    - "midmem"
-    - "midcpu"
    tag: "$id"
  auto:
    simplifyInput: true
@@ -255,8 +256,8 @@ build_info:
  output: "target/executable/tximport"
  executable: "target/executable/tximport/tximport"
  viash_version: "0.9.0"
-  git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
-  git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
+  git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
+  git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "add-labels"
@@ -267,7 +268,7 @@ package_config:
  repositories:
  - type: "vsh"
    name: "biobox"
-    repo: "vsh/biobox"
+    repo: "biobox"
    tag: "main"
  - type: "vsh"
    name: "craftbox"
--- a/target/executable/tximport/tximport
+++ b/target/executable/tximport/tximport
@@ -206,7 +206,7 @@ function ViashHelp {
  echo ""
  echo "    --lengths_gene"
  echo "        type: file, output, file must exist"
-  echo "        default: merged.gene_length.tsv"
+  echo "        default: merged.gene_lengths.tsv"
  echo ""
  echo "    --tpm_transcript"
  echo "        type: file, output, file must exist"
@@ -218,7 +218,7 @@ function ViashHelp {
  echo ""
  echo "    --lengths_transcript"
  echo "        type: file, output, file must exist"
-  echo "        default: merged.transcript_length.tsv"
+  echo "        default: merged.transcript_lengths.tsv"
 }

 # initialise variables
@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component tximport"
-LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
+LABEL org.opencontainers.image.created="2024-12-02T15:00:02Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
 LABEL org.opencontainers.image.version="add-labels"

 VIASHDOCKER
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
              VIASH_PAR_QUANT_RESULTS="$2"
            else
-              VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,""$2"
+              VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;""$2"
            fi
            [ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_results. Use "--help" to get more information on the parameters. && exit 1
            shift 2
@@ -663,7 +663,7 @@ while [[ $# -gt 0 ]]; do
            if [ -z "$VIASH_PAR_QUANT_RESULTS" ]; then
              VIASH_PAR_QUANT_RESULTS=$(ViashRemoveFlags "$1")
            else
-              VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS,"$(ViashRemoveFlags "$1")
+              VIASH_PAR_QUANT_RESULTS="$VIASH_PAR_QUANT_RESULTS;"$(ViashRemoveFlags "$1")
            fi
            shift 1
            ;;
@@ -988,7 +988,7 @@ if [ -z ${VIASH_PAR_COUNTS_GENE_SCALED+x} ]; then
  VIASH_PAR_COUNTS_GENE_SCALED="merged.gene_counts_scaled.tsv"
 fi
 if [ -z ${VIASH_PAR_LENGTHS_GENE+x} ]; then
-  VIASH_PAR_LENGTHS_GENE="merged.gene_length.tsv"
+  VIASH_PAR_LENGTHS_GENE="merged.gene_lengths.tsv"
 fi
 if [ -z ${VIASH_PAR_TPM_TRANSCRIPT+x} ]; then
  VIASH_PAR_TPM_TRANSCRIPT="merged.transcript_tpm.tsv"
@@ -997,12 +997,12 @@ if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPT+x} ]; then
  VIASH_PAR_COUNTS_TRANSCRIPT="merged.transcript_counts.tsv"
 fi
 if [ -z ${VIASH_PAR_LENGTHS_TRANSCRIPT+x} ]; then
-  VIASH_PAR_LENGTHS_TRANSCRIPT="merged.transcript_length.tsv"
+  VIASH_PAR_LENGTHS_TRANSCRIPT="merged.transcript_lengths.tsv"
 fi

 # check whether required files exist
 if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
-  IFS=','
+  IFS=';'
  set -f
  for file in $VIASH_PAR_QUANT_RESULTS; do
    unset IFS
@@ -1145,14 +1145,14 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  VIASH_CHOWN_VARS=()
 if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
  VIASH_TEST_QUANT_RESULTS=()
-  IFS=','
+  IFS=';'
  for var in $VIASH_PAR_QUANT_RESULTS; do
    unset IFS
    VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
    var=$(ViashDockerAutodetectMount "$var")
    VIASH_TEST_QUANT_RESULTS+=( "$var" )
  done
-  VIASH_PAR_QUANT_RESULTS=$(IFS=',' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
+  VIASH_PAR_QUANT_RESULTS=$(IFS=';' ; echo "${VIASH_TEST_QUANT_RESULTS[*]}")
 fi
 if [ ! -z "$VIASH_PAR_TX2GENE_TSV" ]; then
  VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_TX2GENE_TSV")" )
@@ -1303,13 +1303,13 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
 set -eo pipefail

 function clean_up {
-    rm -rf "\$salmon_tmpdir"
+    rm -rf "\$tmpdir"
 }
 trap clean_up EXIT

-tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_functionality_name-XXXXXXXX")
+tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")

-IFS="," read -ra results <<< \$par_quant_results
+IFS=";" read -ra results <<< \$par_quant_results
 for result in \${results[*]}
 do 
    cp -r \$result \$tmpdir
@@ -1333,13 +1333,13 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
  
  if [ ! -z "$VIASH_PAR_QUANT_RESULTS" ]; then
    unset VIASH_TEST_QUANT_RESULTS
-    IFS=','
+    IFS=';'
    for var in $VIASH_PAR_QUANT_RESULTS; do
      unset IFS
      if [ -z "$VIASH_TEST_QUANT_RESULTS" ]; then
      VIASH_TEST_QUANT_RESULTS="$(ViashDockerStripAutomount "$var")"
    else
-      VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS,""$(ViashDockerStripAutomount "$var")"
+      VIASH_TEST_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS;""$(ViashDockerStripAutomount "$var")"
    fi
    done
    VIASH_PAR_QUANT_RESULTS="$VIASH_TEST_QUANT_RESULTS"
--- a/target/executable/tximport/tximport.r
+++ b/target/executable/tximport/tximport.r
@@ -137,5 +137,6 @@ if ("tx2gene" %in% names(transcript_info) && !is.null(transcript_info$tx2gene))
 done <- lapply(params, write_se_table)

 # Output session information and citations
-citation("tximeta")
+# Removed for now because the 'tximeta' package is not found sometimes
+# citation("tximeta") 
 sessionInfo()