From 63c3032a3ba22585f2dc8c08a8a9e228b78c2e2c Mon Sep 17 00:00:00 2001
From: CI <toni@data-intuitive.com>
Date: Tue, 23 Jul 2024 12:29:25 +0000
Subject: [PATCH] Build branch concat_text with version concat_text (341faad)

Build pipeline: viash-hub.craftbox.concat-text-q4j5n

Source commit: https://github.com/viash-hub/craftbox/commit/341faada43ab3ac535e6ebc298ba4c4122ed33cf

Source message: Add authorship
---
 src/_authors/dries_schaumont.yaml             | 11 ++++
 src/_authors/toni_verbeiren.yaml              |  9 +++
 src/concat_text/config.vsh.yaml               | 12 +++-
 src/concat_text/script.sh                     | 10 +--
 src/concat_text/test.sh                       |  8 +--
 .../executable/concat_text/.config.vsh.yaml   | 35 +++++++++-
 target/executable/concat_text/concat_text     | 39 ++++++-----
 target/executable/csv2fasta/.config.vsh.yaml  |  2 +-
 target/executable/csv2fasta/csv2fasta         |  4 +-
 target/executable/untar/.config.vsh.yaml      |  2 +-
 target/executable/untar/untar                 |  4 +-
 target/nextflow/concat_text/.config.vsh.yaml  | 35 +++++++++-
 target/nextflow/concat_text/main.nf           | 66 ++++++++++++++++---
 target/nextflow/concat_text/nextflow.config   |  1 +
 .../nextflow/concat_text/nextflow_schema.json |  2 +-
 target/nextflow/csv2fasta/.config.vsh.yaml    |  2 +-
 target/nextflow/csv2fasta/main.nf             |  2 +-
 target/nextflow/untar/.config.vsh.yaml        |  2 +-
 target/nextflow/untar/main.nf                 |  2 +-
 19 files changed, 196 insertions(+), 52 deletions(-)
 create mode 100644 src/_authors/dries_schaumont.yaml
 create mode 100644 src/_authors/toni_verbeiren.yaml

diff --git a/src/_authors/dries_schaumont.yaml b/src/_authors/dries_schaumont.yaml
new file mode 100644
index 0000000..b267808
--- /dev/null
+++ b/src/_authors/dries_schaumont.yaml
@@ -0,0 +1,11 @@
+name: Dries Schaumont
+info:
+  links:
+    email: dries@data-intuitive.com
+    github: DriesSchaumont
+    orcid: "0000-0002-4389-0440"
+    linkedin: dries-schaumont
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Scientist
diff --git a/src/_authors/toni_verbeiren.yaml b/src/_authors/toni_verbeiren.yaml
new file mode 100644
index 0000000..2f2f851
--- /dev/null
+++ b/src/_authors/toni_verbeiren.yaml
@@ -0,0 +1,9 @@
+name: Toni Verbeiren
+info:
+  links:
+    github: tverbeiren
+    linkedin: verbeiren
+  organizations:
+  - name: Data Intuitive
+    href: https://www.data-intuitive.com
+    role: Data Scientist and CEO
diff --git a/src/concat_text/config.vsh.yaml b/src/concat_text/config.vsh.yaml
index 30bd3e4..6a825ac 100644
--- a/src/concat_text/config.vsh.yaml
+++ b/src/concat_text/config.vsh.yaml
@@ -4,6 +4,16 @@ description: |
   optionally gzip the output text file.
 
   This component is useful for concatening fastq files from different lanes, for instance.
+authors:
+  - __merge__: /src/_authors/toni_verbeiren.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ reviewer ]
+info:
+  improvements: |
+    This component could be improved in 2 ways:
+      1. Allow for a mix of zipped and plain input files
+      2. Allow to specify a compression algorithm for the output
 argument_groups:
   - name: Input arguments
     arguments:
@@ -15,7 +25,7 @@ argument_groups:
         example: input?.txt.gz
   - name: Output arguments
     arguments:
-      - name: "--zip_output"
+      - name: "--gzip_output"
         type: boolean_true
         description: Should the output be zipped?
       - name: --output
diff --git a/src/concat_text/script.sh b/src/concat_text/script.sh
index 9f66766..6c60411 100644
--- a/src/concat_text/script.sh
+++ b/src/concat_text/script.sh
@@ -1,6 +1,6 @@
-#!/bin/bash
+#!/usr/bin/env bash
 
-set -e
+set -euo pipefail
 
 TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
 function clean_up {
@@ -11,10 +11,10 @@ trap clean_up EXIT
 par_input="$(echo "$par_input" | tr ';' ' ')"
 
 echo -n ">> Check if input is gzipped... "
-set +e
+set +eo pipefail
 file $par_input | grep -q 'gzip'
 is_zipped="$?"
-set -e
+set -euo pipefail
 [[ "$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
 if [[ "$is_zipped" == "0" ]]; then
@@ -25,7 +25,7 @@ else
   cat $par_input > $TMPDIR/contents
 fi
 
-if [ "$par_zip_output" == true ]; then
+if [ "$par_gzip_output" == true ]; then
   echo ">> Zip output file"
   gzip $TMPDIR/contents
   mv $TMPDIR/contents.gz $par_output
diff --git a/src/concat_text/test.sh b/src/concat_text/test.sh
index 3549860..1e75223 100644
--- a/src/concat_text/test.sh
+++ b/src/concat_text/test.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-set -eo pipefail
+set -euo pipefail
 
 echo ">> Creating test input files file[1-3].txt"
 INPUT_FILE_1="file1.txt"
@@ -49,7 +49,7 @@ echo ">> Run component on 3 plain input files, zipped output"
 $meta_executable \
   --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
   --output "output3.txt.gz" \
-  --zip_output
+  --gzip_output
 
 [[ ! -f "output3.txt.gz" ]] \
   && echo "Output file output3.txt.gz not found!" && exit 1
@@ -60,11 +60,11 @@ echo ">> Run component on 3 zipped input files, zipped output"
 $meta_executable \
   --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
   --output "output4.txt.gz" \
-  --zip_output
+  --gzip_output
 
 [[ ! -f "output4.txt.gz" ]] \
   && echo "Output file output4.txt.gz not found!" && exit 1
 [[ $(cmp "output4.txt.gz" "expected_output.txt.gz") ]] \
   && echo "Output file output4.txt.gz is not as expected!" && exit 1
 
-echo ">> Tests done, cleaning up"
+echo ">> Tests done"
diff --git a/target/executable/concat_text/.config.vsh.yaml b/target/executable/concat_text/.config.vsh.yaml
index 591c1de..3b72c43 100644
--- a/target/executable/concat_text/.config.vsh.yaml
+++ b/target/executable/concat_text/.config.vsh.yaml
@@ -1,5 +1,31 @@
 name: "concat_text"
 version: "concat_text"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -18,7 +44,7 @@ argument_groups:
 - name: "Output arguments"
   arguments:
   - type: "boolean_true"
-    name: "--zip_output"
+    name: "--gzip_output"
     description: "Should the output be zipped?"
     info: null
     direction: "input"
@@ -45,7 +71,10 @@ test_resources:
 - type: "bash_script"
   path: "test.sh"
   is_executable: true
-info: null
+info:
+  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ for the output\n"
 status: "enabled"
 requirements:
   commands:
@@ -142,7 +171,7 @@ build_info:
   output: "target/executable/concat_text"
   executable: "target/executable/concat_text/concat_text"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/executable/concat_text/concat_text b/target/executable/concat_text/concat_text
index dc94a99..8fac2a2 100755
--- a/target/executable/concat_text/concat_text
+++ b/target/executable/concat_text/concat_text
@@ -10,6 +10,10 @@
 # authors of this component should specify the license in the header of such
 # files, or include a separate license file detailing the licenses of all included
 # files.
+# 
+# Component authors:
+#  * Toni Verbeiren (author, maintainer)
+#  * Dries Schaumont (reviewer)
 
 set -e
 
@@ -186,7 +190,7 @@ function ViashHelp {
   echo "        A list of (gzipped) text files."
   echo ""
   echo "Output arguments:"
-  echo "    --zip_output"
+  echo "    --gzip_output"
   echo "        type: boolean_true"
   echo "        Should the output be zipped?"
   echo ""
@@ -472,10 +476,11 @@ FROM alpine:latest
 ENTRYPOINT []
 RUN apk add --no-cache bash procps file
 
+LABEL org.opencontainers.image.authors="Toni Verbeiren, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component concat_text"
-LABEL org.opencontainers.image.created="2024-07-23T11:57:34Z"
+LABEL org.opencontainers.image.created="2024-07-23T12:21:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5b88b9d8e604ea154a1e952c48a93a203547c18c"
+LABEL org.opencontainers.image.revision="341faada43ab3ac535e6ebc298ba4c4122ed33cf"
 LABEL org.opencontainers.image.version="concat_text"
 
 VIASHDOCKER
@@ -619,9 +624,9 @@ while [[ $# -gt 0 ]]; do
             fi
             shift 1
             ;;
-        --zip_output)
-            [ -n "$VIASH_PAR_ZIP_OUTPUT" ] && ViashError Bad arguments for option \'--zip_output\': \'$VIASH_PAR_ZIP_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_ZIP_OUTPUT=true
+        --gzip_output)
+            [ -n "$VIASH_PAR_GZIP_OUTPUT" ] && ViashError Bad arguments for option \'--gzip_output\': \'$VIASH_PAR_GZIP_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
+            VIASH_PAR_GZIP_OUTPUT=true
             shift 1
             ;;
         --output)
@@ -821,8 +826,8 @@ if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
 fi
 
 # filling in defaults
-if [ -z ${VIASH_PAR_ZIP_OUTPUT+x} ]; then
-  VIASH_PAR_ZIP_OUTPUT="false"
+if [ -z ${VIASH_PAR_GZIP_OUTPUT+x} ]; then
+  VIASH_PAR_GZIP_OUTPUT="false"
 fi
 
 # check whether required files exist
@@ -840,9 +845,9 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
 fi
 
 # check whether parameters values are of the right type
-if [[ -n "$VIASH_PAR_ZIP_OUTPUT" ]]; then
-  if ! [[ "$VIASH_PAR_ZIP_OUTPUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
-    ViashError '--zip_output' has to be a boolean_true. Use "--help" to get more information on the parameters.
+if [[ -n "$VIASH_PAR_GZIP_OUTPUT" ]]; then
+  if ! [[ "$VIASH_PAR_GZIP_OUTPUT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
+    ViashError '--gzip_output' has to be a boolean_true. Use "--help" to get more information on the parameters.
     exit 1
   fi
 fi
@@ -1022,7 +1027,7 @@ cat > "\$tempscript" << 'VIASHMAIN'
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
-$( if [ ! -z ${VIASH_PAR_ZIP_OUTPUT+x} ]; then echo "${VIASH_PAR_ZIP_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_zip_output='&'#" ; else echo "# par_zip_output="; fi )
+$( if [ ! -z ${VIASH_PAR_GZIP_OUTPUT+x} ]; then echo "${VIASH_PAR_GZIP_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_gzip_output='&'#" ; else echo "# par_gzip_output="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -1044,9 +1049,9 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
 
 ## VIASH END
-#!/bin/bash
+#!/usr/bin/env bash
 
-set -e
+set -euo pipefail
 
 TMPDIR=\$(mktemp -d "\$meta_temp_dir/\$meta_functionality_name-XXXXXX")
 function clean_up {
@@ -1057,10 +1062,10 @@ trap clean_up EXIT
 par_input="\$(echo "\$par_input" | tr ';' ' ')"
 
 echo -n ">> Check if input is gzipped... "
-set +e
+set +eo pipefail
 file \$par_input | grep -q 'gzip'
 is_zipped="\$?"
-set -e
+set -euo pipefail
 [[ "\$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
 if [[ "\$is_zipped" == "0" ]]; then
@@ -1071,7 +1076,7 @@ else
   cat \$par_input > \$TMPDIR/contents
 fi
 
-if [ "\$par_zip_output" == true ]; then
+if [ "\$par_gzip_output" == true ]; then
   echo ">> Zip output file"
   gzip \$TMPDIR/contents
   mv \$TMPDIR/contents.gz \$par_output
diff --git a/target/executable/csv2fasta/.config.vsh.yaml b/target/executable/csv2fasta/.config.vsh.yaml
index ee95479..f42b8f7 100644
--- a/target/executable/csv2fasta/.config.vsh.yaml
+++ b/target/executable/csv2fasta/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/executable/csv2fasta"
   executable: "target/executable/csv2fasta/csv2fasta"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/executable/csv2fasta/csv2fasta b/target/executable/csv2fasta/csv2fasta
index 841a2d1..333accf 100755
--- a/target/executable/csv2fasta/csv2fasta
+++ b/target/executable/csv2fasta/csv2fasta
@@ -524,9 +524,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "dnaio"
 
 LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
-LABEL org.opencontainers.image.created="2024-07-23T11:57:33Z"
+LABEL org.opencontainers.image.created="2024-07-23T12:21:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5b88b9d8e604ea154a1e952c48a93a203547c18c"
+LABEL org.opencontainers.image.revision="341faada43ab3ac535e6ebc298ba4c4122ed33cf"
 LABEL org.opencontainers.image.version="concat_text"
 
 VIASHDOCKER
diff --git a/target/executable/untar/.config.vsh.yaml b/target/executable/untar/.config.vsh.yaml
index 8f03e81..919e7a4 100644
--- a/target/executable/untar/.config.vsh.yaml
+++ b/target/executable/untar/.config.vsh.yaml
@@ -147,7 +147,7 @@ build_info:
   output: "target/executable/untar"
   executable: "target/executable/untar/untar"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/executable/untar/untar b/target/executable/untar/untar
index cf43dcb..c3e5542 100755
--- a/target/executable/untar/untar
+++ b/target/executable/untar/untar
@@ -475,9 +475,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component untar"
-LABEL org.opencontainers.image.created="2024-07-23T11:57:34Z"
+LABEL org.opencontainers.image.created="2024-07-23T12:21:54Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
-LABEL org.opencontainers.image.revision="5b88b9d8e604ea154a1e952c48a93a203547c18c"
+LABEL org.opencontainers.image.revision="341faada43ab3ac535e6ebc298ba4c4122ed33cf"
 LABEL org.opencontainers.image.version="concat_text"
 
 VIASHDOCKER
diff --git a/target/nextflow/concat_text/.config.vsh.yaml b/target/nextflow/concat_text/.config.vsh.yaml
index d8c84a3..6071367 100644
--- a/target/nextflow/concat_text/.config.vsh.yaml
+++ b/target/nextflow/concat_text/.config.vsh.yaml
@@ -1,5 +1,31 @@
 name: "concat_text"
 version: "concat_text"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -18,7 +44,7 @@ argument_groups:
 - name: "Output arguments"
   arguments:
   - type: "boolean_true"
-    name: "--zip_output"
+    name: "--gzip_output"
     description: "Should the output be zipped?"
     info: null
     direction: "input"
@@ -45,7 +71,10 @@ test_resources:
 - type: "bash_script"
   path: "test.sh"
   is_executable: true
-info: null
+info:
+  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ for the output\n"
 status: "enabled"
 requirements:
   commands:
@@ -142,7 +171,7 @@ build_info:
   output: "target/nextflow/concat_text"
   executable: "target/nextflow/concat_text/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/nextflow/concat_text/main.nf b/target/nextflow/concat_text/main.nf
index df56e39..05ef370 100644
--- a/target/nextflow/concat_text/main.nf
+++ b/target/nextflow/concat_text/main.nf
@@ -8,6 +8,10 @@
 // authors of this component should specify the license in the header of such
 // files, or include a separate license file detailing the licenses of all included
 // files.
+// 
+// Component authors:
+//  * Toni Verbeiren (author, maintainer)
+//  * Dries Schaumont (reviewer)
 
 ////////////////////////////
 // VDSL3 helper functions //
@@ -2780,6 +2784,49 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "concat_text",
   "version" : "concat_text",
+  "authors" : [
+    {
+      "name" : "Toni Verbeiren",
+      "roles" : [
+        "author",
+        "maintainer"
+      ],
+      "info" : {
+        "links" : {
+          "github" : "tverbeiren",
+          "linkedin" : "verbeiren"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist and CEO"
+          }
+        ]
+      }
+    },
+    {
+      "name" : "Dries Schaumont",
+      "roles" : [
+        "reviewer"
+      ],
+      "info" : {
+        "links" : {
+          "email" : "dries@data-intuitive.com",
+          "github" : "DriesSchaumont",
+          "orcid" : "0000-0002-4389-0440",
+          "linkedin" : "dries-schaumont"
+        },
+        "organizations" : [
+          {
+            "name" : "Data Intuitive",
+            "href" : "https://www.data-intuitive.com",
+            "role" : "Data Scientist"
+          }
+        ]
+      }
+    }
+  ],
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -2805,7 +2852,7 @@ meta = [
       "arguments" : [
         {
           "type" : "boolean_true",
-          "name" : "--zip_output",
+          "name" : "--gzip_output",
           "description" : "Should the output be zipped?",
           "direction" : "input"
         },
@@ -2841,6 +2888,9 @@ meta = [
       "is_executable" : true
     }
   ],
+  "info" : {
+    "improvements" : "This component could be improved in 2 ways:\n  1. Allow for a mix of zipped and plain input files\n  2. Allow to specify a compression algorithm for the output\n"
+  },
   "status" : "enabled",
   "requirements" : {
     "commands" : [
@@ -2955,7 +3005,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/concat_text",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "5b88b9d8e604ea154a1e952c48a93a203547c18c",
+    "git_commit" : "341faada43ab3ac535e6ebc298ba4c4122ed33cf",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
@@ -2998,7 +3048,7 @@ cat > "$tempscript" << VIASHMAIN
 ## VIASH START
 # The following code has been auto-generated by Viash.
 $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
-$( if [ ! -z ${VIASH_PAR_ZIP_OUTPUT+x} ]; then echo "${VIASH_PAR_ZIP_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_zip_output='&'#" ; else echo "# par_zip_output="; fi )
+$( if [ ! -z ${VIASH_PAR_GZIP_OUTPUT+x} ]; then echo "${VIASH_PAR_GZIP_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_gzip_output='&'#" ; else echo "# par_gzip_output="; fi )
 $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi )
 $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
 $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
@@ -3020,9 +3070,9 @@ $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}"
 $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
 
 ## VIASH END
-#!/bin/bash
+#!/usr/bin/env bash
 
-set -e
+set -euo pipefail
 
 TMPDIR=\\$(mktemp -d "\\$meta_temp_dir/\\$meta_functionality_name-XXXXXX")
 function clean_up {
@@ -3033,10 +3083,10 @@ trap clean_up EXIT
 par_input="\\$(echo "\\$par_input" | tr ';' ' ')"
 
 echo -n ">> Check if input is gzipped... "
-set +e
+set +eo pipefail
 file \\$par_input | grep -q 'gzip'
 is_zipped="\\$?"
-set -e
+set -euo pipefail
 [[ "\\$is_zipped" == "0" ]] && echo "yes" || echo "no"
 
 if [[ "\\$is_zipped" == "0" ]]; then
@@ -3047,7 +3097,7 @@ else
   cat \\$par_input > \\$TMPDIR/contents
 fi
 
-if [ "\\$par_zip_output" == true ]; then
+if [ "\\$par_gzip_output" == true ]; then
   echo ">> Zip output file"
   gzip \\$TMPDIR/contents
   mv \\$TMPDIR/contents.gz \\$par_output
diff --git a/target/nextflow/concat_text/nextflow.config b/target/nextflow/concat_text/nextflow.config
index d9194e2..1d6fe37 100644
--- a/target/nextflow/concat_text/nextflow.config
+++ b/target/nextflow/concat_text/nextflow.config
@@ -4,6 +4,7 @@ manifest {
   nextflowVersion = '!>=20.12.1-edge'
   version = 'concat_text'
   description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
+  author = 'Toni Verbeiren, Dries Schaumont'
 }
 
 process.container = 'nextflow/bash:latest'
diff --git a/target/nextflow/concat_text/nextflow_schema.json b/target/nextflow/concat_text/nextflow_schema.json
index 067df29..07a599a 100644
--- a/target/nextflow/concat_text/nextflow_schema.json
+++ b/target/nextflow/concat_text/nextflow_schema.json
@@ -34,7 +34,7 @@
     "properties": {
     
         
-                "zip_output": {
+                "gzip_output": {
                 "type":
                 "boolean",
                 "description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
diff --git a/target/nextflow/csv2fasta/.config.vsh.yaml b/target/nextflow/csv2fasta/.config.vsh.yaml
index 089aa41..886c2c5 100644
--- a/target/nextflow/csv2fasta/.config.vsh.yaml
+++ b/target/nextflow/csv2fasta/.config.vsh.yaml
@@ -222,7 +222,7 @@ build_info:
   output: "target/nextflow/csv2fasta"
   executable: "target/nextflow/csv2fasta/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/nextflow/csv2fasta/main.nf b/target/nextflow/csv2fasta/main.nf
index 423ec9d..d6b87d6 100644
--- a/target/nextflow/csv2fasta/main.nf
+++ b/target/nextflow/csv2fasta/main.nf
@@ -3041,7 +3041,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/csv2fasta",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "5b88b9d8e604ea154a1e952c48a93a203547c18c",
+    "git_commit" : "341faada43ab3ac535e6ebc298ba4c4122ed33cf",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {
diff --git a/target/nextflow/untar/.config.vsh.yaml b/target/nextflow/untar/.config.vsh.yaml
index ed7e023..51d2a17 100644
--- a/target/nextflow/untar/.config.vsh.yaml
+++ b/target/nextflow/untar/.config.vsh.yaml
@@ -147,7 +147,7 @@ build_info:
   output: "target/nextflow/untar"
   executable: "target/nextflow/untar/main.nf"
   viash_version: "0.9.0-RC6"
-  git_commit: "5b88b9d8e604ea154a1e952c48a93a203547c18c"
+  git_commit: "341faada43ab3ac535e6ebc298ba4c4122ed33cf"
   git_remote: "https://github.com/viash-hub/craftbox"
 package_config:
   name: "craftbox"
diff --git a/target/nextflow/untar/main.nf b/target/nextflow/untar/main.nf
index 3639c36..b00d371 100644
--- a/target/nextflow/untar/main.nf
+++ b/target/nextflow/untar/main.nf
@@ -2962,7 +2962,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/untar",
     "viash_version" : "0.9.0-RC6",
-    "git_commit" : "5b88b9d8e604ea154a1e952c48a93a203547c18c",
+    "git_commit" : "341faada43ab3ac535e6ebc298ba4c4122ed33cf",
     "git_remote" : "https://github.com/viash-hub/craftbox"
   },
   "package_config" : {