From 0b04de1cb8a392d674ba7e1485cffcb40457b480 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Fri, 18 Oct 2024 14:00:54 +0200
Subject: [PATCH] remove resources which were moved to common_resources

---
 src/common/comp_tests/check_get_info.py       |   37 -
 src/common/comp_tests/check_method_config.py  |  132 -
 src/common/comp_tests/check_metric_config.py  |  139 -
 src/common/comp_tests/run_and_check_adata.py  |  127 -
 .../helper_functions/read_and_merge_yaml.R    |  144 --
 .../helper_functions/read_and_merge_yaml.py   |   52 -
 .../helper_functions/read_anndata_partial.py  |   77 -
 src/common/helper_functions/read_api_files.R  |  493 ----
 src/common/helper_functions/setup_logger.py   |   12 -
 src/common/helper_functions/strip_margin.R    |    3 -
 src/common/helper_functions/strip_margin.py   |    3 -
 src/common/helper_functions/subset_anndata.py |   83 -
 src/common/schemas/api_component.yaml         |   67 -
 src/common/schemas/api_file.yaml              |   26 -
 src/common/schemas/defs_common.yaml           |  256 --
 src/common/schemas/defs_viash.yaml            | 2252 -----------------
 src/common/schemas/task_control_method.yaml   |   68 -
 src/common/schemas/task_info.yaml             |   22 -
 src/common/schemas/task_method.yaml           |   65 -
 src/common/schemas/task_metric.yaml           |   86 -
 20 files changed, 4144 deletions(-)
 delete mode 100644 src/common/comp_tests/check_get_info.py
 delete mode 100644 src/common/comp_tests/check_method_config.py
 delete mode 100644 src/common/comp_tests/check_metric_config.py
 delete mode 100644 src/common/comp_tests/run_and_check_adata.py
 delete mode 100644 src/common/helper_functions/read_and_merge_yaml.R
 delete mode 100644 src/common/helper_functions/read_and_merge_yaml.py
 delete mode 100644 src/common/helper_functions/read_anndata_partial.py
 delete mode 100644 src/common/helper_functions/read_api_files.R
 delete mode 100644 src/common/helper_functions/setup_logger.py
 delete mode 100644 src/common/helper_functions/strip_margin.R
 delete mode 100644 src/common/helper_functions/strip_margin.py
 delete mode 100644 src/common/helper_functions/subset_anndata.py
 delete mode 100644 src/common/schemas/api_component.yaml
 delete mode 100644 src/common/schemas/api_file.yaml
 delete mode 100644 src/common/schemas/defs_common.yaml
 delete mode 100644 src/common/schemas/defs_viash.yaml
 delete mode 100644 src/common/schemas/task_control_method.yaml
 delete mode 100644 src/common/schemas/task_info.yaml
 delete mode 100644 src/common/schemas/task_method.yaml
 delete mode 100644 src/common/schemas/task_metric.yaml

diff --git a/src/common/comp_tests/check_get_info.py b/src/common/comp_tests/check_get_info.py
deleted file mode 100644
index a00f1d702d..0000000000
--- a/src/common/comp_tests/check_get_info.py
+++ /dev/null
@@ -1,37 +0,0 @@
-import subprocess
-from os import path
-import json
-
-## VIASH START
-## VIASH END
-
-input_path = meta["resources_dir"] + "/test_file.yaml"
-task_id = "denoising"
-output_path = "output.json"
-
-cmd = [
-    meta['executable'],
-    "--input", input_path,
-    "--task_id", task_id,
-    "--output", output_path,
-]
-
-print(">> Running script as test", flush=True)
-out = subprocess.run(cmd, stderr=subprocess.STDOUT)
-
-if out.stdout:
-  print(out.stdout)
-
-if out.returncode:
-  print(f"script: '{cmd}' exited with an error.")
-  exit(out.returncode)
-
-print(">> Checking whether output file exists", flush=True)
-assert path.exists(output_path), "Output does not exist"
-
-print(">> Reading json file", flush=True)
-with open(output_path, 'r') as f:
-    out = json.load(f)
-    print(out)
-
-print("All checks succeeded!", flush=True)
\ No newline at end of file
diff --git a/src/common/comp_tests/check_method_config.py b/src/common/comp_tests/check_method_config.py
deleted file mode 100644
index a30111d648..0000000000
--- a/src/common/comp_tests/check_method_config.py
+++ /dev/null
@@ -1,132 +0,0 @@
-import yaml
-
-## VIASH START
-meta = {
-    "config" : "foo"
-}
-## VIASH END
-
-
-NAME_MAXLEN = 50
-
-SUMMARY_MAXLEN = 400
-
-DESCRIPTION_MAXLEN = 5000
-
-_MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"]
-
-TIME_LABELS = ["lowtime", "midtime", "hightime", "veryhightime"]
-MEM_LABELS = ["lowmem", "midmem", "highmem"]
-CPU_LABELS = ["lowcpu", "midcpu", "highcpu"]
-
-def _load_bib():
-    with open(f"{meta['resources_dir']}/library.bib", "r") as file:
-        return file.read()
-
-def check_url(url):
-    import requests
-    from urllib3.util.retry import Retry
-    from requests.adapters import HTTPAdapter
-
-    # configure retry strategy
-    session = requests.Session()
-    retry = Retry(connect=3, backoff_factor=0.5)
-    adapter = HTTPAdapter(max_retries=retry)
-    session.mount('http://', adapter)
-    session.mount('https://', adapter)
-
-    get = session.head(url)
-
-    if get.ok or get.status_code == 429: # 429 rejected, too many requests
-        return True
-    else:
-        return False
-
-def search_ref_bib(reference):
-    import re
-    bib = _load_bib()
-    
-    entry_pattern =  r"(@\w+{[^}]*" + reference + r"[^}]*}(.|\n)*?)(?=@)"
-
-    bib_entry = re.search(entry_pattern, bib)
-
-    if bib_entry:
-
-        type_pattern = r"@(.*){" + reference
-        doi_pattern = r"(?=[Dd][Oo][Ii]\s*=\s*{([^,}]+)})"
-
-        entry_type = re.search(type_pattern, bib_entry.group(1))
-
-        if not (entry_type.group(1) == "misc" or reference in _MISSING_DOIS):
-            entry_doi = re.search(doi_pattern, bib_entry.group(1))
-            assert entry_doi.group(1), "doi not found in bibtex reference"
-            url = f"https://doi.org/{entry_doi.group(1)}"
-            assert check_url(url), f"{url} is not reachable, ref= {reference}."
-
-        return True
-
-    else:
-        return False
-
-print("Load config data", flush=True)
-with open(meta["config"], "r") as file:
-    config = yaml.safe_load(file)
-
-print("Check general fields", flush=True)
-assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters."
-assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty"
-
-print("Check info fields", flush=True)
-info = config['functionality']['info']
-assert "type" in info, "type not an info field"
-info_types = ["method", "control_method"]
-assert info["type"] in info_types , f"got {info['type']} expected one of {info_types}"
-assert "label" in info is not None, "label not an info field or is empty"
-assert "summary" in info is not None, "summary not an info field or is empty"
-assert "FILL IN:" not in info["summary"], "Summary not filled in"
-assert len(info["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.summary) should not exceed {SUMMARY_MAXLEN} characters."
-assert "description" in info is not None, "description not an info field or is empty"
-assert "FILL IN:" not in info["description"], "description not filled in"
-assert len(info["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.description) should not exceed {DESCRIPTION_MAXLEN} characters."
-if info["type"] == "method":
-    assert "reference" in info, "reference not an info field"
-    bib = _load_bib()
-    if info["reference"]:
-        reference = info["reference"]
-        if not isinstance(reference, list):
-            reference = [reference]
-        for ref in reference:
-            assert search_ref_bib(ref), f"reference {ref} not added to library.bib"
-    assert "documentation_url" in info is not None, "documentation_url not an info field or is empty"
-    assert "repository_url" in info is not None, "repository_url not an info field or is empty"
-    assert check_url(info["documentation_url"]), f"{info['documentation_url']} is not reachable"
-    assert check_url(info["repository_url"]), f"{info['repository_url']} is not reachable"
-
-if "variants" in info:
-    arg_names = [arg["name"].replace("--", "") for arg in config["functionality"]["arguments"]] + ["preferred_normalization"]
-
-    for paramset_id, paramset in info["variants"].items():
-        if paramset:
-            for arg_id in paramset:
-                assert arg_id in arg_names, f"Argument '{arg_id}' in `.functionality.info.variants['{paramset_id}']` is not an argument in `.functionality.arguments`."
-
-assert "preferred_normalization" in info, "preferred_normalization not an info field"
-norm_methods = ["log_cpm", "log_cp10k", "counts", "log_scran_pooling", "sqrt_cpm", "sqrt_cp10k", "l1_sqrt"]
-assert info["preferred_normalization"] in norm_methods, "info['preferred_normalization'] not one of '" + "', '".join(norm_methods) + "'."
-
-print("Check platform fields", flush=True)
-platforms = config['platforms']
-for platform in platforms:
-    if not platform["type"] == "nextflow":
-        continue
-    nextflow= platform
-
-assert nextflow, "nextflow not a platform"
-assert nextflow["directives"], "directives not a field in nextflow platform"
-assert nextflow["directives"]["label"], "label not a field in nextflow platform directives"
-
-assert [i for i in nextflow["directives"]["label"] if i in TIME_LABELS], "time label not filled in"
-assert [i for i in nextflow["directives"]["label"] if i in MEM_LABELS], "mem label not filled in"
-assert [i for i in nextflow["directives"]["label"] if i in CPU_LABELS], "cpu label not filled in"
-
-print("All checks succeeded!", flush=True)
diff --git a/src/common/comp_tests/check_metric_config.py b/src/common/comp_tests/check_metric_config.py
deleted file mode 100644
index 45fa1efc2b..0000000000
--- a/src/common/comp_tests/check_metric_config.py
+++ /dev/null
@@ -1,139 +0,0 @@
-import yaml
-from typing import Dict
-
-## VIASH START
-
-meta = {
-    "config" : "foo"
-}
-
-## VIASH END
-
-NAME_MAXLEN = 50
-
-SUMMARY_MAXLEN = 400
-
-DESCRIPTION_MAXLEN = 5000
-
-_MISSING_DOIS = ["vandermaaten2008visualizing", "hosmer2013applied"]
-
-TIME_LABELS = ["lowtime", "midtime", "hightime"]
-MEM_LABELS = ["lowmem", "midmem", "highmem"]
-CPU_LABELS = ["lowcpu", "midcpu", "highcpu"]
-
-
-def _load_bib():
-    bib_path = meta["resources_dir"]+"/library.bib"
-    with open(bib_path, "r") as file:
-        return file.read()
-    
-def check_url(url):
-    import requests
-    from urllib3.util.retry import Retry
-    from requests.adapters import HTTPAdapter
-
-    # configure retry strategy
-    session = requests.Session()
-    retry = Retry(connect=3, backoff_factor=0.5)
-    adapter = HTTPAdapter(max_retries=retry)
-    session.mount('http://', adapter)
-    session.mount('https://', adapter)
-
-    get = session.head(url)
-
-    if get.ok or get.status_code == 429: # 429 rejected, too many requests
-        return True
-    else:
-        return False
-
-def search_ref_bib(reference):
-    import re
-    bib = _load_bib()
-    
-    entry_pattern =  r"(@\w+{[^}]*" + reference + r"[^}]*}(.|\n)*?)(?=@)"
-
-    bib_entry = re.search(entry_pattern, bib)
-
-    if bib_entry:
-
-        type_pattern = r"@(.*){" + reference
-        doi_pattern = r"(?=[Dd][Oo][Ii]\s*=\s*{([^,}]+)})"
-
-        entry_type = re.search(type_pattern, bib_entry.group(1))
-
-        if not (entry_type.group(1) == "misc" or reference in _MISSING_DOIS):
-            entry_doi = re.search(doi_pattern, bib_entry.group(1))
-            assert entry_doi.group(1), "doi not found in bibtex reference"
-            url = f"https://doi.org/{entry_doi.group(1)}"
-            assert check_url(url), f"{url} is not reachable, ref= {reference}."
-
-        return True
-
-    else:
-        return False
-
-def check_metric(metric: Dict[str, str])  -> str:
-    assert "name" in metric is not None, "name not a field or is empty"
-    assert len(metric["name"]) <= NAME_MAXLEN, f"Component id (.functionality.info.metrics.metric.name) should not exceed {NAME_MAXLEN} characters."
-    assert "label" in metric is not None, "label not a field in metric or is empty"
-    assert "summary" in metric is not None, "summary not a field in metric or is empty"
-    assert "FILL IN:" not in metric["summary"], "Summary not filled in"
-    assert len(metric["summary"]) <= SUMMARY_MAXLEN, f"Component id (.functionality.info.metrics.metric.summary) should not exceed {SUMMARY_MAXLEN} characters."
-    assert "description" in metric is not None, "description not a field in metric or is empty"
-    assert len(metric["description"]) <= DESCRIPTION_MAXLEN, f"Component id (.functionality.info.metrics.metric.description) should not exceed {DESCRIPTION_MAXLEN} characters."
-    assert "FILL IN:" not in metric["description"], "description not filled in"
-    # assert "reference" in metric, "reference not a field in metric"
-    if "reference" in metric:
-        reference = metric["reference"]
-        if not isinstance(reference, list):
-            reference = [reference]
-        for ref in reference:
-            assert search_ref_bib(ref), f"reference {ref} not added to library.bib"
-    # assert "documentation_url" in metric , "documentation_url not a field in metric"
-    # assert "repository_url" in metric , "repository_url not a metric field"
-    if "documentation_url" in metric:
-        assert check_url(metric["documentation_url"]), f"{metric['documentation_url']} is not reachable"
-    if "repository_url" in metric:
-        assert check_url(metric["repository_url"]), f"{metric['repository_url']} is not reachable"
-    assert "min" in metric is not None, f"min not a field in metric or is emtpy"
-    assert "max" in metric is not None, f"max not a field in metric or is empty"
-    assert "maximize" in metric is not None, f"maximize not a field in metric or is emtpy"
-    assert isinstance(metric['min'], (int, str)), "not an int or string (-.inf)"
-    assert isinstance(metric['max'], (int, str)), "not an int or string (+.inf)"
-    assert isinstance(metric['maximize'], bool) or metric["maximize"] not in ["-inf", "+inf"], "not a bool"
-
-
-print("Load config data", flush=True)
-with open(meta["config"], "r") as file:
-                config = yaml.safe_load(file)
-
-print("check general fields", flush=True)
-assert "name" in config["functionality"] is not None, "Name not a field or is empty"
-assert len(config["functionality"]["name"]) <= NAME_MAXLEN, f"Component id (.functionality.name) should not exceed {NAME_MAXLEN} characters."
-assert "namespace" in config["functionality"] is not None, "namespace not a field or is empty"
-
-
-print("Check info fields", flush=True)
-info = config['functionality']['info']
-assert "type" in info, "type not an info field"
-assert info["type"] == "metric" , f"got {info['type']} expected 'metric'"
-assert "metrics" in info, "metrics not an info field"
-for metric in info["metrics"]:
-    check_metric(metric)
-
-print("Check platform fields", flush=True)
-platforms = config['platforms']
-for platform in platforms:
-    if not platform["type"] == "nextflow":
-        continue
-    nextflow= platform
-
-assert nextflow, "nextflow not a platform"
-assert nextflow["directives"], "directives not a field in nextflow platform"
-assert nextflow["directives"]["label"], "label not a field in nextflow platform directives"
-
-assert [i for i in nextflow["directives"]["label"] if i in TIME_LABELS], "time label not filled in"
-assert [i for i in nextflow["directives"]["label"] if i in MEM_LABELS], "mem label not filled in"
-assert [i for i in nextflow["directives"]["label"] if i in CPU_LABELS], "cpu label not filled in"
-
-print("All checks succeeded!", flush=True)
diff --git a/src/common/comp_tests/run_and_check_adata.py b/src/common/comp_tests/run_and_check_adata.py
deleted file mode 100644
index d2cda5af94..0000000000
--- a/src/common/comp_tests/run_and_check_adata.py
+++ /dev/null
@@ -1,127 +0,0 @@
-import anndata as ad
-import subprocess
-from os import path
-import yaml
-import re
-
-## VIASH START
-meta = {
-    "executable": "target/docker/denoising/methods/dca/dca",
-    "config": "target/docker/denoising/methods/dca/.config.vsh.yaml",
-    "resources_dir": "resources_test/denoising"
-}
-## VIASH END
-
-# helper functions
-def check_slots(adata, arg):
-    """Check whether an AnnData file contains all for the required
-    slots in the corresponding .info.slots field.
-    """
-    for struc_name, slot_items in arg["info"].get("slots", {}).items():
-        struc_x = getattr(adata, struc_name)
-        
-        if struc_name == "X":
-            if slot_items.get("required", True):
-                assert struc_x is not None,\
-                    f"File '{arg['value']}' is missing slot .{struc_name}"
-        
-        else:
-            for slot_item in slot_items:
-                if slot_item.get("required", True):
-                    assert slot_item["name"] in struc_x,\
-                        f"File '{arg['value']}' is missing slot .{struc_name}['{slot_item['name']}']"
-
-def run_and_check(arguments, cmd):
-    print(">> Checking whether input files exist", flush=True)
-    for arg in arguments:
-        if arg["type"] == "file" and arg["direction"] == "input":
-            assert path.exists(arg["value"]), f"Input file '{arg['value']}' does not exist"
-
-    print(f">> Running script as test", flush=True)
-    out = subprocess.run(cmd, stderr=subprocess.STDOUT)
-
-    if out.stdout:
-        print(out.stdout)
-
-    if out.returncode:
-        print(f"script: \'{' '.join(cmd)}\' exited with an error.")
-        exit(out.returncode)
-
-    print(">> Checking whether output file exists", flush=True)
-    for arg in arguments:
-        if arg["type"] == "file" and arg["direction"] == "output":
-            assert path.exists(arg["value"]), f"Output file '{arg['value']}' does not exist"
-
-    print(">> Reading h5ad files and checking formats", flush=True)
-    adatas = {}
-    for arg in arguments:
-        if arg["type"] == "file" and "slots" in arg["info"]:
-            print(f"Reading and checking {arg['clean_name']}", flush=True)
-            adata = ad.read_h5ad(arg["value"])
-
-            print(f"  {adata}")
-
-            check_slots(adata, arg)
-
-            adatas[arg["clean_name"]] = adata
-
-    print("All checks succeeded!", flush=True)
-
-
-# read viash config
-with open(meta["config"], "r") as file:
-    config = yaml.safe_load(file)
-
-# get resources
-arguments = []
-
-for arg in config["functionality"]["arguments"]:
-    new_arg = arg.copy()
-    arg_info = new_arg.get("info") or {}
-
-    # set clean name
-    clean_name = re.sub("^--", "", arg["name"])
-    new_arg["clean_name"] = clean_name
-
-    # use example to find test resource file
-    if arg["type"] == "file":
-      if arg["direction"] == "input":
-          value = f"{meta['resources_dir']}/{arg['example'][0]}"
-      else:
-          value = f"{clean_name}.h5ad"
-      new_arg["value"] = value
-    elif "test_default" in arg_info:
-        new_arg["value"] = arg_info["test_default"]
-        
-    arguments.append(new_arg)
-
-
-if "test_setup" not in config["functionality"]["info"]:
-    argument_sets = {"run": arguments}
-else:
-    test_setup = config["functionality"]["info"]["test_setup"]
-    argument_sets = {}
-    for name, test_instance in test_setup.items():
-        new_arguments = []
-        for arg in arguments:
-            new_arg = arg.copy()
-            if arg["clean_name"] in test_instance:
-                val = test_instance[arg["clean_name"]]
-                if new_arg["type"] == "file" and new_arg["direction"] == "input":
-                    val = f"{meta['resources_dir']}/{val}"
-                new_arg["value"] = val
-            new_arguments.append(new_arg)
-        argument_sets[name] = new_arguments
-
-for argset_name, argset_args in argument_sets.items():
-    print(f">> Running test '{argset_name}'", flush=True)
-    # construct command
-    cmd = [ meta["executable"] ]
-    for arg in argset_args:
-        if "value" in arg:
-            value = arg["value"]
-            if arg["multiple"] and isinstance(value, list):
-                value = arg["multiple_sep"].join(value)
-            cmd.extend([arg["name"], str(value)])
-
-    run_and_check(argset_args, cmd)
\ No newline at end of file
diff --git a/src/common/helper_functions/read_and_merge_yaml.R b/src/common/helper_functions/read_and_merge_yaml.R
deleted file mode 100644
index 932d3feb92..0000000000
--- a/src/common/helper_functions/read_and_merge_yaml.R
+++ /dev/null
@@ -1,144 +0,0 @@
-#' Read a Viash YAML
-#'
-#' If the YAML contains a "__merge__" key anywhere in the yaml,
-#' the path specified in that YAML will be read and the two
-#' lists will be merged. This is a recursive procedure.
-#'
-#' @param path Path to Viash YAML
-read_and_merge_yaml <- function(path, project_path = .ram_find_project(path)) {
-  path <- normalizePath(path, mustWork = FALSE)
-  data <- tryCatch({
-    suppressWarnings(yaml::read_yaml(path))
-  }, error = function(e) {
-    stop("Could not read ", path, ". Error: ", e)
-  })
-  .ram_process_merge(data, data, path, project_path)
-}
-
-.ram_find_project <- function(path) {
-  path <- normalizePath(path, mustWork = FALSE)
-  check <- paste0(dirname(path), "/_viash.yaml")
-  if (file.exists(check)) {
-    dirname(check)
-  } else if (check == "//_viash.yaml") {
-    NULL
-  } else {
-    .ram_find_project(dirname(check))
-  }
-}
-
-.ram_is_named_list <- function(obj) {
-  is.null(obj) || (is.list(obj) && (length(obj) == 0 || !is.null(names(obj))))
-}
-
-.ram_process_merge <- function(data, root_data, path, project_path) {
-  if (.ram_is_named_list(data)) {
-    # check whether children have `__merge__` entries
-    processed_data <- lapply(data, function(dat) {
-      .ram_process_merge(dat, root_data, path, project_path)
-    })
-    processed_data <- lapply(names(data), function(nm) {
-      dat <- data[[nm]]
-      .ram_process_merge(dat, root_data, path, project_path)
-    })
-    names(processed_data) <- names(data)
-
-    # if current element has __merge__, read list2 yaml and combine with data
-    new_data <-
-      if ("__merge__" %in% names(processed_data) && !.ram_is_named_list(processed_data$`__merge__`)) {
-        new_data_path <- .ram_resolve_path(
-          path = processed_data$`__merge__`,
-          project_path = project_path,
-          parent_path = dirname(path)
-        )
-        read_and_merge_yaml(new_data_path, project_path)
-      } else if ("$ref" %in% names(processed_data) && !.ram_is_named_list(processed_data$`$ref`)) {
-        ref_parts <- strsplit(processed_data$`$ref`, "#")[[1]]
-
-        # resolve the path in $ref
-        x <-
-          if (ref_parts[[1]] == "") {
-            root_data
-          } else {
-            new_data_path <- .ram_resolve_path(
-              path = ref_parts[[1]],
-              project_path = project_path,
-              parent_path = dirname(path)
-            )
-            new_data_path <- normalizePath(new_data_path, mustWork = FALSE)
-
-            # read in the new data
-            tryCatch({
-              suppressWarnings(yaml::read_yaml(new_data_path))
-            }, error = function(e) {
-              stop("Could not read ", new_data_path, ". Error: ", e)
-            })
-          }
-        x_root <- x
-        
-
-        # Navigate the path and retrieve the referenced data
-        ref_path_parts <- unlist(strsplit(ref_parts[[2]], "/"))
-        for (part in ref_path_parts) {
-          if (part == "") {
-            next
-          } else if (part %in% names(x)) {
-            x <- x[[part]]
-          } else {
-            stop("Could not find ", processed_data$`$ref`, " in ", path)
-          }
-        }
-
-        # postprocess the new data
-        if (ref_parts[[1]] == "") {
-          x
-        } else {
-          .ram_process_merge(x, x_root, new_data_path, project_path)
-        }
-      } else {
-        list()
-      }
-
-    .ram_deep_merge(new_data, processed_data)
-  } else if (is.list(data)) {
-    lapply(data, function(dat) {
-      .ram_process_merge(dat, root_data, path, project_path)
-    })
-  } else {
-    data
-  }
-}
-
-.ram_resolve_path <- function(path, project_path, parent_path) {
-  ifelse(
-    grepl("^/", path),
-    paste0(project_path, "/", path),
-    fs::path_abs(path, parent_path)
-  )
-}
-
-.ram_deep_merge <- function(list1, list2) {
-  if (.ram_is_named_list(list1) && .ram_is_named_list(list2)) {
-    # if list1 and list2 are objects, recursively merge
-    keys <- unique(c(names(list1), names(list2)))
-    out <- lapply(keys, function(key) {
-      if (key %in% names(list1)) {
-        if (key %in% names(list2)) {
-          .ram_deep_merge(list1[[key]], list2[[key]])
-        } else {
-          list1[[key]]
-        }
-      } else {
-        list2[[key]]
-      }
-    })
-    names(out) <- keys
-    out
-  } else if (is.list(list1) && is.list(list2)) {
-    # if list1 and list2 are both lists, append
-    c(list1, list2)
-  } else {
-    # else override list1 with list2
-    list2
-  }
-}
\ No newline at end of file
diff --git a/src/common/helper_functions/read_and_merge_yaml.py b/src/common/helper_functions/read_and_merge_yaml.py
deleted file mode 100644
index b74995aed1..0000000000
--- a/src/common/helper_functions/read_and_merge_yaml.py
+++ /dev/null
@@ -1,52 +0,0 @@
-def read_and_merge_yaml(path):
-    """Read a Viash YAML
-    
-    If the YAML contains a "__merge__" key anywhere in the yaml,
-    the path specified in that YAML will be read and the two
-    lists will be merged. This is a recursive procedure.
-    
-    Arguments:
-    path -- Path to the Viash YAML"""
-    from ruamel.yaml import YAML
-
-    yaml = YAML(typ='safe', pure=True)
-
-    with open(path, 'r') as stream:
-        data = yaml.load(stream)
-    return _ram_process_merge(data, path)
-
-def _ram_deep_merge(dict1, dict2):
-    if isinstance(dict1, dict) and isinstance(dict2, dict):
-        keys = set(list(dict1.keys()) + list(dict2.keys()))
-        out = {}
-        for key in keys:
-            if key in dict1:
-                if key in dict2:
-                    out[key] = _ram_deep_merge(dict1[key], dict2[key])
-                else:
-                    out[key] = dict1[key]
-            else:
-                out[key] = dict2[key]
-        return out
-    elif isinstance(dict1, list) and isinstance(dict2, list):
-        return dict1 + dict2
-    else:
-        return dict2
-
-def _ram_process_merge(data, path):
-    import os
-    if isinstance(data, dict):
-        processed_data = {k: _ram_process_merge(v, path) for k, v in data.items()}
-
-        if "__merge__" in processed_data:
-            new_data_path = os.path.join(os.path.dirname(path), processed_data["__merge__"])
-            new_data = read_and_merge_yaml(new_data_path)
-        else:
-            new_data = {}
-
-        return _ram_deep_merge(new_data, processed_data)
-    elif isinstance(data, list):
-        return [_ram_process_merge(dat, path) for dat in data]
-    else:
-        return data
-
diff --git a/src/common/helper_functions/read_anndata_partial.py b/src/common/helper_functions/read_anndata_partial.py
deleted file mode 100644
index efbea0592d..0000000000
--- a/src/common/helper_functions/read_anndata_partial.py
+++ /dev/null
@@ -1,77 +0,0 @@
-import warnings
-from pathlib import Path
-import anndata as ad
-import h5py
-from scipy.sparse import csr_matrix
-from anndata.experimental import read_elem, sparse_dataset
-
-
-def read_anndata(
-    file: str,
-    backed: bool = False,
-    **kwargs
-) -> ad.AnnData:
-    """
-    Read anndata file
-    :param file: path to anndata file in h5ad format
-    :param kwargs: AnnData parameter to group mapping
-    """
-    assert Path(file).exists(), f'File not found: {file}'
-    
-    f = h5py.File(file, 'r')
-    kwargs = {x: x for x in f} if not kwargs else kwargs
-    if len(f.keys()) == 0:
-        return ad.AnnData()
-    # check if keys are available
-    for name, slot in kwargs.items():
-        if slot not in f:
-            warnings.warn(
-                f'Cannot find "{slot}" for AnnData parameter `{name}` from "{file}"'
-            )
-    adata = read_partial(f, backed=backed, **kwargs)
-    if not backed:
-        f.close()
-    
-    return adata
-
-
-def read_partial(
-    group: h5py.Group,
-    backed: bool = False,
-    force_sparse_types: [str, list] = None,
-    **kwargs
-) -> ad.AnnData:
-    """
-    Partially read h5py groups
-    :params group: file group
-    :params force_sparse_types: encoding types to convert to sparse_dataset via csr_matrix
-    :params backed: read sparse matrix as sparse_dataset
-    :params **kwargs: dict of slot_name: slot, by default use all available slot for the h5py file
-    :return: AnnData object
-    """
-    if force_sparse_types is None:
-        force_sparse_types = []
-    elif isinstance(force_sparse_types, str):
-        force_sparse_types = [force_sparse_types]
-    slots = {}
-    if backed:
-        print('Read as backed sparse matrix...')
-    
-    for slot_name, slot in kwargs.items():
-        print(f'Read slot "{slot}", store as "{slot_name}"...')
-        if slot not in group:
-            warnings.warn(f'Slot "{slot}" not found, skip...')
-            slots[slot_name] = None
-        else:
-            elem = group[slot]
-            iospec = ad._io.specs.get_spec(elem)
-            if iospec.encoding_type in ("csr_matrix", "csc_matrix") and backed:
-                slots[slot_name] = sparse_dataset(elem)
-            elif iospec.encoding_type in force_sparse_types:
-                slots[slot_name] = csr_matrix(read_elem(elem))
-                if backed:
-                    slots[slot_name] = sparse_dataset(slots[slot_name])
-            else:
-                slots[slot_name] = read_elem(elem)
-    return ad.AnnData(**slots)
-
diff --git a/src/common/helper_functions/read_api_files.R b/src/common/helper_functions/read_api_files.R
deleted file mode 100644
index f2cf49b2f8..0000000000
--- a/src/common/helper_functions/read_api_files.R
+++ /dev/null
@@ -1,493 +0,0 @@
-
-anndata_struct_names <- c("obs", "var", "obsm", "obsp", "varm", "varp", "layers", "uns")
-
-read_file_spec <- function(path) {
-  spec <- read_and_merge_yaml(path)
-  out <- list(
-    info = read_file_info(spec, path)
-  )
-  if (out$info$file_type == "h5ad" || "slots" %in% names(spec$info)) {
-    out$info$file_type <- "h5ad"
-    out$slots <- read_anndata_slots(spec, path)
-  }
-  if (out$info$file_type == "csv" || out$info$file_type == "tsv" || out$info$file_type == "parquet") {
-    out$columns <- read_tabular_columns(spec, path)
-  }
-  out
-}
-read_file_info <- function(spec, path) {
-  # TEMP: make it readable
-  spec$info$slots <- NULL
-  df <- list_as_tibble(spec)
-  if (list_contains_tibble(spec$info)) {
-    df <- dplyr::bind_cols(df, list_as_tibble(spec$info))
-  }
-  df$file_name <- basename(path) %>% gsub("\\.yaml", "", .)
-  df$description <- df$description %||% NA_character_ %>% as.character
-  df$summary <- df$summary %||% NA_character_ %>% as.character
-  as_tibble(df)
-}
-read_anndata_slots <- function(spec, path) {
-  map_df(
-    anndata_struct_names,
-    function(struct_name, slot) {
-      slot <- spec$info$slots[[struct_name]]
-      if (is.null(slot)) return(NULL)
-      df <- map_df(slot, as.data.frame)
-      df$struct <- struct_name
-      df$file_name <- basename(path) %>% gsub("\\.yaml", "", .)
-      df$required <- df$required %||% TRUE %|% TRUE
-      df$multiple <- df$multiple %||% FALSE %|% FALSE
-      as_tibble(df)
-    }
-  )
-}
-read_tabular_columns <- function(spec, path) {
-  map_df(
-    spec$info$columns,
-    function(column) {
-      df <- list_as_tibble(column)
-      df$file_name <- basename(path) %>% gsub("\\.yaml", "", .)
-      df$required <- df$required %||% TRUE %|% TRUE
-      df$multiple <- df$multiple %||% FALSE %|% FALSE
-      as_tibble(df)
-    }
-  )
-}
-
-format_file_format <- function(spec) {
-  if (spec$info$file_type == "h5ad") {
-    example <- spec$slots %>%
-      group_by(struct) %>%
-      summarise(
-        str = paste0(unique(struct), ": ", paste0("'", name, "'", collapse = ", "))
-      ) %>%
-      arrange(match(struct, anndata_struct_names))
-
-    c("    AnnData object", paste0("     ", example$str))
-  } else if (spec$info$file_type == "csv" || spec$info$file_type == "tsv" || spec$info$file_type == "parquet") {
-    example <- spec$columns %>%
-      summarise(
-        str = paste0("'", name, "'", collapse = ", ")
-      )
-
-    c("    Tabular data", paste0("     ", example$str))
-  } else {
-    ""
-  }
-}
-
-format_file_format_as_kable <- function(spec) {
-  if (spec$info$file_type == "h5ad") {
-    spec$slots %>%
-      mutate(
-        tag_str = pmap_chr(lst(required), function(required) {
-          out <- c()
-          if (!required) {
-            out <- c(out, "Optional")
-          }
-          if (length(out) == 0) {
-            ""
-          } else {
-            paste0("(_", paste(out, collapse = ", "), "_) ")
-          }
-        })
-      ) %>%
-      transmute(
-        Slot = paste0("`", struct, "[\"", name, "\"]`"),
-        Type = paste0("`", type, "`"),
-        Description = paste0(
-          tag_str,
-          description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), 
-          "."
-        )
-      ) %>%
-      knitr::kable()
-  } else if (spec$info$file_type == "csv" || spec$info$file_type == "tsv" || spec$info$file_type == "parquet") {
-    spec$columns %>%
-      mutate(
-        tag_str = pmap_chr(lst(required), function(required) {
-          out <- c()
-          if (!required) {
-            out <- c(out, "Optional")
-          }
-          if (length(out) == 0) {
-            ""
-          } else {
-            paste0("(_", paste(out, collapse = ", "), "_) ")
-          }
-        })
-      ) %>%
-      transmute(
-        Column = paste0("`", name, "`"),
-        Type = paste0("`", type, "`"),
-        Description = paste0(
-          tag_str,
-          description %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), 
-          "."
-        )
-      ) %>%
-      knitr::kable()
-  } else {
-    ""
-  }
-}
-
-list_contains_tibble <- function(li) {
-  is.list(li) && any(sapply(li, is.atomic))
-}
-
-list_as_tibble <- function(li) {
-  as.data.frame(li[sapply(li, is.atomic)], check.names = FALSE)
-}
-
-read_comp_spec <- function(path) {
-  spec_yaml <- read_and_merge_yaml(path)
-  list(
-    info = read_comp_info(spec_yaml, path),
-    args = read_comp_args(spec_yaml, path)
-  )
-}
-
-read_comp_info <- function(spec_yaml, path) {
-  # TEMP: make it readable
-  spec_yaml$functionality$arguments <- NULL
-  spec_yaml$functionality$argument_groups <- NULL
-  
-  df <- list_as_tibble(spec_yaml$functionality)
-  if (nrow(df) == 0) {
-    df <- data.frame(a = 1)[, integer(0)]
-  }
-  if (list_contains_tibble(spec_yaml$functionality$info)) {
-    df <- dplyr::bind_cols(df, list_as_tibble(spec_yaml$functionality$info))
-  }
-  if (list_contains_tibble(spec_yaml$functionality$info$type_info)) {
-    df <- dplyr::bind_cols(df, list_as_tibble(spec_yaml$functionality$info$type_info))
-  }
-  df$file_name <- basename(path) %>% gsub("\\.yaml", "", .)
-  as_tibble(df)
-}
-
-read_comp_args <- function(spec_yaml, path) {
-  arguments <- spec_yaml$functionality$arguments
-  for (arg_group in spec_yaml$functionality$argument_groups) {
-    arguments <- c(arguments, arg_group$arguments)
-  }
-  map_df(arguments, function(arg) {
-    df <- list_as_tibble(arg)
-    if (list_contains_tibble(arg$info)) {
-      df <- dplyr::bind_cols(df, list_as_tibble(arg$info))
-    }
-    df$file_name <- basename(path) %>% gsub("\\.yaml", "", .)
-    df$arg_name <- gsub("^-*", "", arg$name)
-    df$direction <- df$direction %||% "input" %|% "input"
-    df$parent <- df$`__merge__` %||% NA_character_ %>% basename() %>% gsub("\\.yaml", "", .)
-    df$required <- df$required %||% FALSE %|% FALSE
-    df$default <- df$default %||% NA_character_ %>% as.character
-    df$example <- df$example %||% NA_character_ %>% as.character
-    df$description <- df$description %||% NA_character_ %>% as.character
-    df$summary <- df$summary %||% NA_character_ %>% as.character
-    df
-  })
-}
-
-format_comp_args_as_tibble <- function(spec) {
-  if (nrow(spec$args) == 0) return("")
-  spec$args %>%
-    mutate(
-      tag_str = pmap_chr(lst(required, direction), function(required, direction) {
-        out <- c()
-        if (!required) {
-          out <- c(out, "Optional")
-        }
-        if (direction == "output") {
-          out <- c(out, "Output")
-        }
-        if (length(out) == 0) {
-          ""
-        } else {
-          paste0("(_", paste(out, collapse = ", "), "_) ")
-        }
-      })
-    ) %>%
-    transmute(
-      Name = paste0("`--", arg_name, "`"),
-      Type = paste0("`", type, "`"),
-      Description = paste0(
-        tag_str,
-        (summary %|% description) %>% gsub(" *\n *", " ", .) %>% gsub("\\. *$", "", .), 
-        ".",
-        ifelse(!is.na(default), paste0(" Default: `", default, "`."), "")
-      )
-    ) %>%
-    knitr::kable()
-}
-
-# path <- "src/datasets/api/comp_processor_knn.yaml"
-render_component <- function(spec) {
-  if (is.character(spec)) {
-    spec <- read_comp_spec(spec)
-  }
-
-  strip_margin(glue::glue("
-    §## Component type: {spec$info$label}
-    §
-    §Path: [`src/{spec$info$namespace}`](https://github.com/openproblems-bio/openproblems/tree/main/src/{spec$info$namespace})
-    §
-    §{spec$info$summary}
-    §
-    §Arguments:
-    §
-    §:::{{.small}}
-    §{paste(format_comp_args_as_tibble(spec), collapse = '\n')}
-    §:::
-    §
-    §"), symbol = "§")
-}
-
-# path <- "src/datasets/api/file_pca.yaml"
-render_file <- function(spec) {
-  if (is.character(spec)) {
-    spec <- read_file_spec(spec)
-  }
-
-  if (!"label" %in% names(spec$info)) {
-    spec$info$label <- basename(spec$info$example)
-  }
-
-  example <-
-    if (is.null(spec$info$example) || is.na(spec$info$example)) {
-      ""
-    } else {
-      paste0("Example file: `", spec$info$example, "`")
-    }
-
-  description <-
-    if (is.null(spec$info$description) || is.na(spec$info$description)) {
-      ""
-    } else {
-      paste0("Description:\n\n", spec$info$description)
-    }
-
-  strip_margin(glue::glue("
-    §## File format: {spec$info$label}
-    §
-    §{spec$info$summary %||% ''}
-    §
-    §{example}
-    §
-    §{description}
-    §
-    §Format:
-    §
-    §:::{{.small}}
-    §{paste(format_file_format(spec), collapse = '\n')}
-    §:::
-    §
-    §Slot description:
-    §
-    §:::{{.small}}
-    §{paste(format_file_format_as_kable(spec), collapse = '\n')}
-    §:::
-    §
-    §"), symbol = "§")
-}
-
-# path <- "src/tasks/denoising"
-read_task_api <- function(path) {
-  cli::cli_inform("Looking for project root")
-  project_path <- .ram_find_project(path)
-  api_dir <- paste0(path, "/api")
-
-  cli::cli_inform("Reading task info")
-  task_info_yaml <- list.files(api_dir, pattern = "task_info.ya?ml", full.names = TRUE)
-  assertthat::assert_that(length(task_info_yaml) == 1)
-  task_info <- read_and_merge_yaml(task_info_yaml, project_path)
-
-  cli::cli_inform("Reading task authors")
-  authors <- map_df(task_info$authors, function(aut) {
-    aut$roles <- paste(aut$roles, collapse = ", ")
-    list_as_tibble(aut)
-  })
-
-  cli::cli_inform("Reading component yamls")
-  comp_yamls <- list.files(api_dir, pattern = "comp_.*\\.ya?ml", full.names = TRUE)
-  comps <- map(comp_yamls, read_comp_spec)
-  comp_info <- map_df(comps, "info")
-  comp_args <- map_df(comps, "args")
-  names(comps) <- basename(comp_yamls) %>% gsub("\\..*$", "", .)
-
-  cli::cli_inform("Reading file yamls")
-  file_yamls <- .ram_resolve_path(
-    path = na.omit(unique(comp_args$`__merge__`)),
-    project_path = project_path,
-    parent_path = api_dir
-  )
-  files <- map(file_yamls, read_file_spec)
-  names(files) <- basename(file_yamls) %>% gsub("\\..*$", "", .)
-  file_info <- map_df(files, "info")
-  file_slots <- map_df(files, "slots")
-
-  cli::cli_inform("Generating task graph")
-  task_graph <- create_task_graph(file_info, comp_info, comp_args)
-
-  list(
-    task_info = task_info,
-    file_specs = files,
-    file_info = file_info,
-    file_slots = file_slots,
-    comp_specs = comps,
-    comp_info = comp_info,
-    comp_args = comp_args,
-    task_graph = task_graph,
-    authors = authors
-  )
-}
-
-
-create_task_graph <- function(file_info, comp_info, comp_args) {
-  clean_id <- function(id) {
-    gsub("graph", "graaf", id)
-  }
-  nodes <-
-    bind_rows(
-      file_info %>%
-        mutate(id = file_name, label = label, is_comp = FALSE),
-      comp_info %>%
-        mutate(id = file_name, label = label, is_comp = TRUE)
-    ) %>%
-      select(id, label, everything()) %>%
-      mutate(str = paste0(
-        "  ",
-        clean_id(id),
-        ifelse(is_comp, "[/\"", "(\""),
-        label,
-        ifelse(is_comp, "\"/]", "\")")
-      ))
-  edges <- bind_rows(
-    comp_args %>%
-      filter(type == "file", direction == "input") %>%
-      mutate(
-        from = parent,
-        to = file_name,
-        arrow = "---"
-      ),
-    comp_args %>%
-      filter(type == "file", direction == "output") %>%
-      mutate(
-        from = file_name,
-        to = parent,
-        arrow = "-->"
-      )
-  ) %>%
-    select(from, to, everything()) %>%
-    mutate(str = paste0("  ", clean_id(from), arrow, clean_id(to)))
-
-  igraph::graph_from_data_frame(
-    edges,
-    vertices = nodes,
-    directed = TRUE
-  )
-}
-
-.task_graph_get_root <- function(task_api) {
-  root <- names(which(igraph::degree(task_api$task_graph, mode = "in") == 0))
-  if (length(root) > 1) {
-    warning(
-      "There should probably only be one node with in-degree equal to 0.\n",
-      "  Nodes with in-degree == 0: ", paste(root, collapse = ", ")
-    )
-  }
-  root[[1]]
-}
-
-render_task_graph <- function(task_api, root = .task_graph_get_root(task_api)) {
-  order <- names(igraph::bfs(task_api$task_graph, root)$order)
-
-  vdf <- igraph::as_data_frame(task_api$task_graph, "vertices") %>%
-    arrange(match(name, order))
-  edf <- igraph::as_data_frame(task_api$task_graph, "edges") %>%
-    arrange(match(from, order), match(to, order))
-
-  strip_margin(glue::glue("
-    §```mermaid
-    §flowchart LR
-    §{paste(vdf$str, collapse = '\n')}
-    §{paste(edf$str, collapse = '\n')}
-    §```
-    §"), symbol = "§")
-}
-
-
-
-# Recursive function to process each property with indentation
-.render_example_process_property <- function(prop, prop_name = NULL, indent_level = 0) {
-  if (is.null(prop_name)) {
-    prop_name <- ""
-  }
-
-  out <- c()
-
-  # define helper variables
-  indent_spaces <- strrep(" ", indent_level)
-  next_indent_spaces <- strrep(" ", indent_level + 2)
-
-  # add comment if available
-  if ("description" %in% names(prop)) {
-    comment <- gsub("\n", paste0("\n", indent_spaces, "# "), stringr::str_trim(prop$description))
-    out <- c(out, indent_spaces, "# ", comment, "\n")
-  }
-
-  # add variable
-  out <- c(out, indent_spaces, prop_name, ": ")
-
-  if (prop$type == "object" && "properties" %in% names(prop)) {
-    # Handle object with properties
-    prop_names <- setdiff(names(prop$properties), "additionalProperties")
-    sub_props <- unlist(lapply(prop_names, function(sub_prop_name) {
-      prop_out <- .render_example_process_property(
-        prop$properties[[sub_prop_name]],
-        sub_prop_name,
-        indent_level + 2
-      )
-      c(prop_out, "\n")
-    }))
-    c(out, "\n", sub_props[-length(sub_props)])
-  } else if (prop$type == "array") {
-    if (is.list(prop$items) && "properties" %in% names(prop$items)) {
-      # Handle array of objects
-      array_items_yaml <- unlist(lapply(names(prop$items$properties), function(item_prop_name) {
-        prop_out <- .render_example_process_property(
-          prop$items$properties[[item_prop_name]],
-          item_prop_name,
-          indent_level + 4
-        )
-        c(prop_out, "\n")
-      }))
-      c(out, "\n", next_indent_spaces, "- ", array_items_yaml[-1])
-    } else {
-      # Handle simple array
-      c(out, "[ ... ]")
-    }
-  } else {
-    c(out, "...")
-  }
-}
-
-# Function for rendering an example yaml based on a JSON schema
-render_example <- function(json_schema) {
-  if (!"properties" %in% names(json_schema)) {
-    return("")
-  }
-  text <-
-    unlist(lapply(names(json_schema$properties), function(prop_name) {
-      out <- .render_example_process_property(
-        json_schema$properties[[prop_name]],
-        prop_name,
-        0
-      )
-      c(out, "\n")
-    }))
-
-  paste(text, collapse = "")
-}
\ No newline at end of file
diff --git a/src/common/helper_functions/setup_logger.py b/src/common/helper_functions/setup_logger.py
deleted file mode 100644
index ae71eb9611..0000000000
--- a/src/common/helper_functions/setup_logger.py
+++ /dev/null
@@ -1,12 +0,0 @@
-def setup_logger():
-    import logging
-    from sys import stdout
-
-    logger = logging.getLogger()
-    logger.setLevel(logging.INFO)
-    console_handler = logging.StreamHandler(stdout)
-    logFormatter = logging.Formatter("%(asctime)s %(levelname)-8s %(message)s")
-    console_handler.setFormatter(logFormatter)
-    logger.addHandler(console_handler)
-
-    return logger
\ No newline at end of file
diff --git a/src/common/helper_functions/strip_margin.R b/src/common/helper_functions/strip_margin.R
deleted file mode 100644
index 3830d58d79..0000000000
--- a/src/common/helper_functions/strip_margin.R
+++ /dev/null
@@ -1,3 +0,0 @@
-strip_margin <- function(text, symbol = "\\|") {
-  gsub(paste0("(^|\n)[ \t]*", symbol), "\\1", text)
-}
\ No newline at end of file
diff --git a/src/common/helper_functions/strip_margin.py b/src/common/helper_functions/strip_margin.py
deleted file mode 100644
index fbfb39dec9..0000000000
--- a/src/common/helper_functions/strip_margin.py
+++ /dev/null
@@ -1,3 +0,0 @@
-def strip_margin(text: str) -> str:
-  import re
-  return re.sub("(^|\n)[ \t]*\|", "\\1", text)
\ No newline at end of file
diff --git a/src/common/helper_functions/subset_anndata.py b/src/common/helper_functions/subset_anndata.py
deleted file mode 100644
index 80bd160872..0000000000
--- a/src/common/helper_functions/subset_anndata.py
+++ /dev/null
@@ -1,83 +0,0 @@
-"""Helper functions related to subsetting AnnData objects based on the file format 
-specifications in the .config.vsh.yaml and slot mapping overrides."""
-
-def read_config_slots_info(config_file, slot_mapping = {}):
-    """Read the .config.vsh.yaml to find out which output slots need to be copied to which output file.
-    
-    Arguments:
-    config_file -- Path to the .config.vsh.yaml file (required).
-    slot_mapping -- Which slots to retain. Must be a dictionary whose keys are the names 
-      of the AnnData structs, and values is another dictionary with destination value
-      names as keys and source value names as values.
-      Example of slot_mapping: 
-        ```
-        slot_mapping = {
-          "layers": {
-            "counts": par["layer_counts"],
-          },
-          "obs": {
-            "cell_type": par["obs_cell_type"],
-            "batch": par["obs_batch"],
-          }
-        }
-        ```
-    """
-    import yaml
-    import re
-
-    # read output spec from yaml
-    with open(config_file, "r") as object_name:
-        config = yaml.safe_load(object_name)
-
-    output_struct_slots = {}
-
-    # fetch info on which slots should be copied to which file
-    for arg in config["functionality"]["arguments"]:
-        # argument is an output file with a slot specification
-        if arg["direction"] == "output" and arg.get("info", {}).get("slots"):
-            object_name = re.sub("--", "", arg["name"])
-            
-            struct_slots = arg['info']['slots']
-            out = {}
-            for (struct, slots) in struct_slots.items():
-                out_struct = {}
-                for slot in slots:
-                    # if slot_mapping[struct][slot['name']] exists, use that as the source slot name
-                    # otherwise use slot['name']
-                    source_slot = slot_mapping.get(struct, {}).get(slot["name"], slot["name"])
-                    out_struct[slot["name"]] = source_slot
-                out[struct] = out_struct
-
-            output_struct_slots[object_name] = out
-
-    return output_struct_slots
-
-# create new anndata objects according to api spec
-def subset_anndata(adata, slot_info):
-    """Create new anndata object according to slot info specifications.
-    
-    Arguments:
-    adata -- An AnnData object to subset (required)
-    slot_info -- Which slots to retain, typically one of the items in the output of read_config_slots_info.
-      Must be a dictionary whose keys are the names of the AnnData structs, and values is another 
-      dictionary with destination value names as keys and source value names as values. 
-      """
-    import pandas as pd
-    import anndata as ad
-
-    structs = ["layers", "obs", "var", "uns", "obsp", "obsm", "varp", "varm"]
-    kwargs = {}
-
-    for struct in structs:
-        slot_mapping = slot_info.get(struct, {})
-        data = {dest : getattr(adata, struct)[src] for (dest, src) in slot_mapping.items()}
-        if len(data) > 0:
-            if struct in ['obs', 'var']:
-                data = pd.concat(data, axis=1)
-            kwargs[struct] = data
-        elif struct in ['obs', 'var']:
-            # if no columns need to be copied, we still need an 'obs' and a 'var' 
-            # to help determine the shape of the adata
-            kwargs[struct] = getattr(adata, struct).iloc[:,[]]
-
-    return ad.AnnData(**kwargs)
\ No newline at end of file
diff --git a/src/common/schemas/api_component.yaml b/src/common/schemas/api_component.yaml
deleted file mode 100644
index b197e2e367..0000000000
--- a/src/common/schemas/api_component.yaml
+++ /dev/null
@@ -1,67 +0,0 @@
-title: Component API
-description: |
-  A component type specification file.
-type: object
-required: [functionality]
-properties:
-  functionality:
-    type: object
-    description: Information regarding the functionality of the component.
-    required: [namespace, info, arguments, test_resources]
-    additionalProperties: false
-    properties:
-      namespace:
-        "$ref": "defs_common.yaml#/definitions/Namespace"
-      info:
-        type: object
-        description: Metadata of the component.
-        additionalProperties: false
-        required: [type, type_info]
-        properties:
-          type:
-            "$ref": "defs_common.yaml#/definitions/ComponentType"
-          subtype:
-            "$ref": "defs_common.yaml#/definitions/ComponentSubtype"
-          type_info:
-            type: object
-            description: Metadata related to the component type.
-            required: [label, summary, description]
-            properties:
-              label:
-                $ref: "defs_common.yaml#/definitions/Label"
-              summary: 
-                $ref: "defs_common.yaml#/definitions/Summary"
-              description: 
-                $ref: "defs_common.yaml#/definitions/Description"
-      arguments:
-        type: array
-        description: Component-specific parameters.
-        items:
-          anyOf:
-            - $ref: 'defs_common.yaml#/definitions/ComponentAPIFile'
-            - $ref: 'defs_viash.yaml#/definitions/BooleanArgument'
-            - $ref: 'defs_viash.yaml#/definitions/BooleanArgument'
-            - $ref: 'defs_viash.yaml#/definitions/BooleanTrueArgument'
-            - $ref: 'defs_viash.yaml#/definitions/BooleanFalseArgument'
-            - $ref: 'defs_viash.yaml#/definitions/DoubleArgument'
-            - $ref: 'defs_viash.yaml#/definitions/IntegerArgument'
-            - $ref: 'defs_viash.yaml#/definitions/LongArgument'
-            - $ref: 'defs_viash.yaml#/definitions/StringArgument'
-      resources:
-        type: array
-        description: Resources required to run the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-      test_resources:
-        type: array
-        description: One or more scripts and resources used to test the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-  platforms:
-    type: array
-    description: A list of platforms which Viash generates target artifacts for.
-    items:
-      anyOf:
-        - "$ref": "defs_common.yaml#/definitions/PlatformDocker"
-        - "$ref": "defs_common.yaml#/definitions/PlatformNative"
-        - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3"
diff --git a/src/common/schemas/api_file.yaml b/src/common/schemas/api_file.yaml
deleted file mode 100644
index 6294439eda..0000000000
--- a/src/common/schemas/api_file.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-title: File API
-description: A file format specification file.
-type: object
-additionalProperties: false
-required: [type, example, info]
-properties:
-  type:
-    const: file
-  example:
-    description: A file in the `resources_test` folder which is an example of this file format.
-    type: string
-  __merge__:
-    $ref: "defs_common.yaml#/definitions/Merge"
-  info:
-    description: 'Structured information. Can be any shape: a string, vector, map or even nested map.'
-    type: object
-    required: [label, summary]
-    properties:
-      label:
-        $ref: "defs_common.yaml#/definitions/Label"
-      summary: 
-        $ref: "defs_common.yaml#/definitions/Summary"
-      description: 
-        $ref: "defs_common.yaml#/definitions/Description"
-      slots:
-        $ref: "defs_common.yaml#/definitions/AnnDataSlots"
diff --git a/src/common/schemas/defs_common.yaml b/src/common/schemas/defs_common.yaml
deleted file mode 100644
index 60b9946210..0000000000
--- a/src/common/schemas/defs_common.yaml
+++ /dev/null
@@ -1,256 +0,0 @@
-definitions:
-  PlatformVdsl3:
-    title: VDSL3
-    description: Next-gen platform for generating NextFlow VDSL3 modules.
-    properties:
-      type:
-        const: nextflow
-        description: Next-gen platform for generating NextFlow VDSL3 modules.
-      directives:
-        $ref: 'defs_viash.yaml#/definitions/NextflowDirectives'
-    required: [ type ]
-    additionalProperties: false
-  PlatformDocker:
-    title: Docker platform
-    description: |
-      Run a Viash component on a Docker backend platform.
-      By specifying which dependencies your component needs, users are be able to build
-      a docker container from scratch using the setup flag, or pull it from a docker repository.
-    type: object
-    properties:
-      type:
-        const: docker
-        description: Run a Viash component on a Docker backend platform.
-      image:
-        type: string
-        description: The base container to start from. You can also add the tag here
-          if you wish.
-      run_args:
-        anyOf:
-        - type: string
-          description: Add docker run arguments.
-        - type: array
-          items:
-            type: string
-          description: Add docker run arguments.
-      target_image_source:
-        type: string
-        description: The source of the target image. This is used for defining labels
-          in the dockerfile.
-      setup:
-        type: array
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Requirements"
-      test_setup:
-        type: array
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Requirements"
-    required: [type, image]
-    additionalProperties: false
-  PlatformNative:
-    title: Native platform
-    type: object
-    properties:
-      type:
-        const: native
-        description: Specifies the type of the platform. Running a Viash component
-          on a native platform means that the script will be executed in your current
-          environment.
-    required: [ type ]
-    additionalProperties: false
-  PreferredNormalization:
-    enum: [l1_sqrt, log_cpm, log_cp10k, log_scran_pooling, sqrt_cpm, sqrt_cp10k, counts]
-    description: |
-      Which normalization method a component prefers. 
-      
-      Each value corresponds to a normalization component in the directory `src/datasets/normalization`.
-  ComponentSubtype:
-    type: string
-    description: |
-      A component subtype, in case the task has multiple subtypes of methods and metrics.
-  ComponentType:
-    type: string
-    description: |
-      A component subtype, in case the task has multiple subtypes of methods and metrics.
-  Name:
-    type: string
-    description: |
-      A unique identifier. Can only contain lowercase letters, numbers or underscores.
-    pattern: "^[a-z_][a-z0-9_]*$"
-    maxLength: 50
-  Namespace:
-    type: string
-    description: |
-      The namespace a component is part of.
-    pattern: "^[a-z_][a-z0-9_/]*$"
-  Label:
-    type: string
-    description: |
-      A unique, human-readable, short label. Used for creating summary tables and visualisations.
-    maxLength: 50
-  Image:
-    type: string
-    description: |
-      The name of the image file to use for the component on the website.
-  Summary:
-    type: string
-    description: |
-      A one sentence summary of purpose and methodology. Used for creating an overview tables.
-    minLength: 15
-    maxLength: 180
-  Description:
-    type: string
-    description: |
-      A longer description (one or more paragraphs). Used for creating reference documentation and supplementary information.
-    minLength: 30
-  BibtexReference:
-    type: string
-    description: |
-      A bibtex reference key to the paper where the component is described.
-  DocumentationURL:
-    type: string
-    format: uri
-    pattern: "^https://"
-    description: The url to the documentation of the used software library.
-  RepositoryURL:
-    type: string
-    format: uri
-    pattern: "^https://"
-    description: The url to the repository of the used software library.
-  MethodVariants:
-    type: object
-    description: Alternative parameter sets which should be evaluated in the benchmark.
-    properties:
-      preferred_normalization:
-        "$ref": "#/definitions/PreferredNormalization"
-  CompAPIMerge:
-    type: string
-    description: |
-      The API specifies which type of component this is.
-      It contains specifications for:
-
-        - The input/output files
-        - Common parameters
-        - A unit test
-  Merge:
-    type: string
-    description: |
-      Another YAML to inherit values from.
-  ComponentAPIFile:
-    description: A `file` type argument has a string value that points to a file or folder path.
-    type: object
-    properties:
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f` or `foo`. The number of dashes determines how values can be passed:  \n\n  - `--foo` is a long option, which can be passed with `executable_name --foo=value` or `executable_name --foo value`\n  - `-f` is a short option, which can be passed with `executable_name -f value`\n  - `foo` is an argument, which can be passed with `executable_name value`  \n"
-        type: string
-      __merge__:
-        type: string
-        description: The file format specification file.
-      direction:
-        description: Makes this argument an `input` or an `output`, as in does the file/folder needs to be read or written. `input` by default.
-        $ref: 'defs_viash.yaml#/definitions/Direction'
-      info:
-        description: 'Structured information. Can be any shape: a string, vector, map or even nested map.'
-        type: object
-      required:
-        description: Make the value for this argument required. If set to `true`, an error will be produced if no value was provided. `false` by default.
-        type: boolean
-    required: [name, __merge__, direction, required]
-    additionalProperties: false
-  AnnDataSlots:
-    properties:
-      X:
-        $ref: "#/definitions/AnnDataSlot"
-      layers:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      var:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      varm:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      varp:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      obs:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      obsm:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      obsp:
-        type: array
-        items:
-          $ref: "#/definitions/AnnDataSlot"
-      uns:
-        type: array
-        items:
-          oneOf:
-            - $ref: "#/definitions/AnnDataSlot"
-            - $ref: "#/definitions/AnnDataSlotObject"
-  AnnDataSlot:
-    properties:
-      type:
-        enum: [integer, double, string, boolean]
-      name:
-        type: string
-        description: A unique identifier.
-        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
-      description:
-        type: string
-      required:
-        type: boolean
-    required: [type, name, description, required]
-  AnnDataSlotObject:
-    properties:
-      type:
-        enum: [object]
-      name:
-        type: string
-        description: A unique identifier.
-        pattern: "^[a-zA-Z_][a-zA-Z0-9_]*$"
-      description:
-        type: string
-      required:
-        type: boolean
-    required: [type, name, description, required]
-  Author:
-    description: Author metadata.
-    type: object
-    additionalProperties: false
-    properties:
-      name:
-        description: Full name of the author, usually in the name of FirstName MiddleName LastName.
-        type: string
-      info:
-        description: Additional information on the author
-        type: object
-        additionalProperties: false
-        properties:
-          github:
-            type: string
-          orcid:
-            type: string
-          email:
-            type: string
-          twitter:
-            type: string
-          linkedin:
-            type: string
-      roles:
-        description: |
-            Role of the author. Possible values:
-
-            * `"author"`: Authors who have made substantial contributions to the component.
-            * `"maintainer"`: The maintainer of the component.
-            * `"contributor"`: Authors who have made smaller contributions (such as code patches etc.).
-        type: array
-        items:
-          enum: [maintainer, author, contributor]
\ No newline at end of file
diff --git a/src/common/schemas/defs_viash.yaml b/src/common/schemas/defs_viash.yaml
deleted file mode 100644
index fff25ab382..0000000000
--- a/src/common/schemas/defs_viash.yaml
+++ /dev/null
@@ -1,2252 +0,0 @@
-$schema: "https://json-schema.org/draft-07/schema#"
-title: Viash config schema definitions.
-oneOf:
-  - $ref: "#/definitions/Config"
-definitions:
-  Config:
-    description: "A Viash Config"
-    properties:
-      functionality:
-        description: "The functionality-part of the config file describes the behaviour\
-          \ of the script in terms of arguments and resources.\nBy specifying a few restrictions\
-          \ (e.g. mandatory arguments) and adding some descriptions, Viash will automatically\
-          \ generate a stylish command-line interface for you.\n"
-        $ref: "#/definitions/Functionality"
-      platforms:
-        description: "Definition of the platforms"
-        type: "array"
-        items:
-          $ref: "#/definitions/Platforms"
-      info:
-        description: "Definition of meta data"
-        $ref: "#/definitions/Info"
-    required:
-    - "functionality"
-    additionalProperties: false
-  NativePlatform:
-    description: "Running a Viash component on a native platform means that the script\
-      \ will be executed in your current environment.\nAny dependencies are assumed\
-      \ to have been installed by the user, so the native platform is meant for developers\
-      \ (who know what they're doing) or for simple bash scripts (which have no extra\
-      \ dependencies).\n"
-    type: "object"
-    properties:
-      id:
-        description: "As with all platforms, you can give a platform a different name.\
-          \ By specifying `id: foo`, you can target this platform (only) by specifying\
-          \ `-p foo` in any of the Viash commands."
-        type: "string"
-      type:
-        description: "Running a Viash component on a native platform means that the\
-          \ script will be executed in your current environment.\nAny dependencies\
-          \ are assumed to have been installed by the user, so the native platform\
-          \ is meant for developers (who know what they're doing) or for simple bash\
-          \ scripts (which have no extra dependencies).\n"
-        const: "native"
-    required:
-    - "type"
-    additionalProperties: false
-  DockerPlatform:
-    description: "Run a Viash component on a Docker backend platform.\nBy specifying\
-      \ which dependencies your component needs, users will be able to build a docker\
-      \ container from scratch using the setup flag, or pull it from a docker repository.\n"
-    type: "object"
-    properties:
-      organization:
-        description: "Name of a container's [organization](https://docs.docker.com/docker-hub/orgs/)."
-        type: "string"
-      registry:
-        description: "The URL to the a [custom Docker registry](https://docs.docker.com/registry/)"
-        type: "string"
-      image:
-        description: "The base container to start from. You can also add the tag here\
-          \ if you wish."
-        type: "string"
-      tag:
-        description: "Specify a Docker image based on its tag."
-        type: "string"
-      target_tag:
-        description: "The tag the resulting image gets. Advanced usage only."
-        type: "string"
-      run_args:
-        anyOf:
-        - description: "Add [docker run](https://docs.docker.com/engine/reference/run/)\
-            \ arguments."
-          type: "string"
-        - description: "Add [docker run](https://docs.docker.com/engine/reference/run/)\
-            \ arguments."
-          type: "array"
-          items:
-            type: "string"
-      namespace_separator:
-        description: "The separator between the namespace and the name of the component,\
-          \ used for determining the image name. Default: `\"/\"`."
-        type: "string"
-      resolve_volume:
-        description: "Enables or disables automatic volume mapping. Enabled when set\
-          \ to `Automatic` or disabled when set to `Manual`. Default: `Automatic`."
-        $ref: "#/definitions/DockerResolveVolume"
-      port:
-        anyOf:
-        - description: "A list of enabled ports. This doesn't change the Dockerfile\
-            \ but gets added as a command-line argument at runtime."
-          type: "string"
-        - description: "A list of enabled ports. This doesn't change the Dockerfile\
-            \ but gets added as a command-line argument at runtime."
-          type: "array"
-          items:
-            type: "string"
-      setup:
-        description: "A list of requirements for installing the following types of\
-          \ packages:\n\n - @[apt](apt_req)\n - @[apk](apk_req)\n - @[Docker setup\
-          \ instructions](docker_req)\n - @[JavaScript](javascript_req)\n - @[Python](python_req)\n\
-          \ - @[R](r_req)\n - @[Ruby](ruby_req)\n - @[yum](yum_req)\n\nThe order in\
-          \ which these dependencies are specified determines the order in which they\
-          \ will be installed.\n"
-        type: "array"
-        items:
-          $ref: "#/definitions/Requirements"
-      workdir:
-        description: "The working directory when starting the container. This doesn't\
-          \ change the Dockerfile but gets added as a command-line argument at runtime."
-        type: "string"
-      target_image:
-        description: "If anything is specified in the setup section, running the `---setup`\
-          \ will result in an image with the name of `<target_image>:<version>`. If\
-          \ nothing is specified in the `setup` section, simply `image` will be used.\
-          \ Advanced usage only."
-        type: "string"
-      cmd:
-        anyOf:
-        - description: "Set the default command being executed when running the Docker\
-            \ container."
-          type: "string"
-        - description: "Set the default command being executed when running the Docker\
-            \ container."
-          type: "array"
-          items:
-            type: "string"
-      target_image_source:
-        description: "The source of the target image. This is used for defining labels\
-          \ in the dockerfile."
-        type: "string"
-      test_setup:
-        description: "Additional requirements specific for running unit tests."
-        type: "array"
-        items:
-          $ref: "#/definitions/Requirements"
-      entrypoint:
-        anyOf:
-        - description: "Override the entrypoint of the base container. Default set\
-            \ `ENTRYPOINT []`."
-          type: "string"
-        - description: "Override the entrypoint of the base container. Default set\
-            \ `ENTRYPOINT []`."
-          type: "array"
-          items:
-            type: "string"
-      id:
-        description: "As with all platforms, you can give a platform a different name.\
-          \ By specifying `id: foo`, you can target this platform (only) by specifying\
-          \ `-p foo` in any of the Viash commands."
-        type: "string"
-      target_registry:
-        description: "The URL where the resulting image will be pushed to. Advanced\
-          \ usage only."
-        type: "string"
-      setup_strategy:
-        description: "The Docker setup strategy to use when building a container.\n\
-          \n| Strategy | Description |\n|-----|----------|\n| `alwaysbuild` / `build`\
-          \ / `b` | Always build the image from the dockerfile. This is the default\
-          \ setup strategy.\n| `alwayscachedbuild` / `cachedbuild` / `cb` | Always\
-          \ build the image from the dockerfile, with caching enabled.\n| `ifneedbebuild`\
-          \ |  Build the image if it does not exist locally.\n| `ifneedbecachedbuild`\
-          \ | Build the image with caching enabled if it does not exist locally, with\
-          \ caching enabled.\n| `alwayspull` / `pull` / `p` |  Try to pull the container\
-          \ from [Docker Hub](https://hub.docker.com) or the @[specified docker registry](docker_registry).\n\
-          | `alwayspullelsebuild` / `pullelsebuild` |  Try to pull the image from\
-          \ a registry and build it if it doesn't exist.\n| `alwayspullelsecachedbuild`\
-          \ / `pullelsecachedbuild` |  Try to pull the image from a registry and build\
-          \ it with caching if it doesn't exist.\n| `ifneedbepull` |  If the image\
-          \ does not exist locally, pull the image.\n| `ifneedbepullelsebuild` | \
-          \ If the image does not exist locally, pull the image. If the image does\
-          \ exist, build it.\n| `ifneedbepullelsecachedbuild` | If the image does\
-          \ not exist locally, pull the image. If the image does exist, build it with\
-          \ caching enabled.\n| `push` | Push the container to [Docker Hub](https://hub.docker.com)\
-          \  or the @[specified docker registry](docker_registry).\n| `pushifnotpresent`\
-          \ | Push the container to [Docker Hub](https://hub.docker.com) or the @[specified\
-          \ docker registry](docker_registry) if the @[tag](docker_tag) does not exist\
-          \ yet.\n| `donothing` / `meh` | Do not build or pull anything.\n\n"
-        $ref: "#/definitions/DockerSetupStrategy"
-      type:
-        description: "Run a Viash component on a Docker backend platform.\nBy specifying\
-          \ which dependencies your component needs, users will be able to build a\
-          \ docker container from scratch using the setup flag, or pull it from a\
-          \ docker repository.\n"
-        const: "docker"
-      target_organization:
-        description: "The organization set in the resulting image. Advanced usage\
-          \ only."
-        type: "string"
-      chown:
-        description: "In Linux, files created by a Docker container will be owned\
-          \ by `root`. With `chown: true`, Viash will automatically change the ownership\
-          \ of output files (arguments with `type: file` and `direction: output`)\
-          \ to the user running the Viash command after execution of the component.\
-          \ Default value: `true`."
-        type: "boolean"
-    required:
-    - "image"
-    - "type"
-    additionalProperties: false
-  NextflowVdsl3Platform:
-    description: "Next-gen platform for generating NextFlow VDSL3 modules."
-    type: "object"
-    properties:
-      auto:
-        description: "@[Automated processing flags](nextflow_auto) which can be toggled\
-          \ on or off:\n\n| Flag | Description | Default |\n|---|---------|----|\n\
-          | `simplifyInput` | If `true`, an input tuple only containing only a single\
-          \ File (e.g. `[\"foo\", file(\"in.h5ad\")]`) is automatically transformed\
-          \ to a map (i.e. `[\"foo\", [ input: file(\"in.h5ad\") ] ]`). | `true` |\n\
-          | `simplifyOutput` | If `true`, an output tuple containing a map with a\
-          \ File (e.g. `[\"foo\", [ output: file(\"out.h5ad\") ] ]`) is automatically\
-          \ transformed to a map (i.e. `[\"foo\", file(\"out.h5ad\")]`). | `true`\
-          \ |\n| `transcript` | If `true`, the module's transcripts from `work/` are\
-          \ automatically published to `params.transcriptDir`. If not defined, `params.publishDir\
-          \ + \"/_transcripts\"` will be used. Will throw an error if neither are\
-          \ defined. | `false` |\n| `publish` | If `true`, the module's outputs are\
-          \ automatically published to `params.publishDir`.  Will throw an error if\
-          \ `params.publishDir` is not defined. | `false` |\n\n"
-        $ref: "#/definitions/NextflowAuto"
-      directives:
-        description: "@[Directives](nextflow_directives) are optional settings that\
-          \ affect the execution of the process. These mostly match up with the Nextflow\
-          \ counterparts.  \n"
-        $ref: "#/definitions/NextflowDirectives"
-      container:
-        description: "Specifies the Docker platform id to be used to run Nextflow."
-        type: "string"
-      debug:
-        description: "Whether or not to print debug messages."
-        type: "boolean"
-      id:
-        description: "Every platform can be given a specific id that can later be\
-          \ referred to explicitly when running or building the Viash component."
-        type: "string"
-      type:
-        description: "Next-gen platform for generating NextFlow VDSL3 modules."
-        const: "nextflow"
-      config:
-        description: "Allows tweaking how the @[Nextflow Config](nextflow_config)\
-          \ file is generated."
-        $ref: "#/definitions/NextflowConfig"
-    required:
-    - "type"
-    additionalProperties: false
-  Platforms:
-    anyOf:
-    - $ref: "#/definitions/NativePlatform"
-    - $ref: "#/definitions/DockerPlatform"
-    - $ref: "#/definitions/NextflowVdsl3Platform"
-  Info:
-    description: "Meta information fields filled in by Viash during build."
-    type: "object"
-    properties:
-      git_tag:
-        description: "Git tag."
-        type: "string"
-      git_remote:
-        description: "Git remote name."
-        type: "string"
-      viash_version:
-        description: "The Viash version that was used to build the component."
-        type: "string"
-      config:
-        description: "Path to the config used during build."
-        type: "string"
-      output:
-        description: "Folder path to the build artifacts."
-        type: "string"
-      platform:
-        description: "The platform id used during build."
-        type: "string"
-      git_commit:
-        description: "Git commit hash."
-        type: "string"
-      executable:
-        description: "Output folder with main executable path."
-        type: "string"
-    required:
-    - "config"
-    additionalProperties: false
-  Functionality:
-    description: "The functionality-part of the config file describes the behaviour\
-      \ of the script in terms of arguments and resources.\nBy specifying a few restrictions\
-      \ (e.g. mandatory arguments) and adding some descriptions, Viash will automatically\
-      \ generate a stylish command-line interface for you.\n"
-    type: "object"
-    properties:
-      name:
-        description: "Name of the component and the filename of the executable when\
-          \ built with `viash build`."
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      version:
-        description: "Version of the component. This field will be used to version\
-          \ the executable and the Docker container."
-        type: "string"
-      authors:
-        description: "A list of @[authors](author). An author must at least have a\
-          \ name, but can also have a list of roles, an e-mail address, and a map\
-          \ of custom properties.\n\nSuggested values for roles are:\n \n| Role |\
-          \ Abbrev. | Description |\n|------|---------|-------------|\n| maintainer\
-          \ | mnt | for the maintainer of the code. Ideally, exactly one maintainer\
-          \ is specified. |\n| author | aut | for persons who have made substantial\
-          \ contributions to the software. |\n| contributor | ctb| for persons who\
-          \ have made smaller contributions (such as code patches).\n| datacontributor\
-          \ | dtc | for persons or organisations that contributed data sets for the\
-          \ software\n| copyrightholder | cph | for all copyright holders. This is\
-          \ a legal concept so should use the legal name of an institution or corporate\
-          \ body.\n| funder | fnd | for persons or organizations that furnished financial\
-          \ support for the development of the software\n\nThe [full list of roles](https://www.loc.gov/marc/relators/relaterm.html)\
-          \ is extremely comprehensive.\n"
-        type: "array"
-        items:
-          $ref: "#/definitions/Author"
-      status:
-        description: "Allows setting a component to active, deprecated or disabled."
-        $ref: "#/definitions/Status"
-      requirements:
-        description: "@[Computational requirements](computational_requirements) related\
-          \ to running the component. \n`cpus` specifies the maximum number of (logical)\
-          \ cpus a component is allowed to use., whereas\n`memory` specifies the maximum\
-          \ amount of memory a component is allowed to allicate. Memory units must\
-          \ be\nin B, KB, MB, GB, TB or PB."
-        $ref: "#/definitions/ComputationalRequirements"
-      resources:
-        description: "@[Resources](resources) are files that support the component.\
-          \ The first resource should be @[a script](scripting_languages) that will\
-          \ be executed when the functionality is run. Additional resources will be\
-          \ copied to the same directory.\n\nCommon properties:\n\n * type: `file`\
-          \ / `r_script` / `python_script` / `bash_script` / `javascript_script` /\
-          \ `scala_script` / `csharp_script`, specifies the type of the resource.\
-          \ The first resource cannot be of type `file`. When the type is not specified,\
-          \ the default type is simply `file`.\n * dest: filename, the resulting name\
-          \ of the resource.  From within a script, the file can be accessed at `meta[\"\
-          resources_dir\"] + \"/\" + dest`. If unspecified, `dest` will be set to\
-          \ the basename of the `path` parameter.\n * path: `path/to/file`, the path\
-          \ of the input file. Can be a relative or an absolute path, or a URI. Mutually\
-          \ exclusive with `text`.\n * text: ...multiline text..., the content of\
-          \ the resulting file specified as a string. Mutually exclusive with `path`.\n\
-          \ * is_executable: `true` / `false`, whether the resulting resource file\
-          \ should be made executable.\n"
-        type: "array"
-        items:
-          $ref: "#/definitions/Resource"
-      test_resources:
-        description: "One or more @[scripts](scripting_languages) to be used to test\
-          \ the component behaviour when `viash test` is invoked. Additional files\
-          \ of type `file` will be made available only during testing. Each test script\
-          \ should expect no command-line inputs, be platform-independent, and return\
-          \ an exit code >0 when unexpected behaviour occurs during testing. See @[Unit\
-          \ Testing](unit_testing) for more info."
-        type: "array"
-        items:
-          $ref: "#/definitions/Resource"
-      argument_groups:
-        description: "A grouping of the @[arguments](argument), used to display the\
-          \ help message.\n\n - `name: foo`, the name of the argument group. \n -\
-          \ `description: Description of foo`, a description of the argument group.\
-          \ Multiline descriptions are supported.\n - `arguments: [arg1, arg2, ...]`,\
-          \ list of the arguments names.\n\n"
-        type: "array"
-        items:
-          $ref: "#/definitions/ArgumentGroup"
-      description:
-        description: "A description of the component. This will be displayed with\
-          \ `--help`."
-        type: "string"
-      usage:
-        description: "A description on how to use the component. This will be displayed\
-          \ with `--help` under the 'Usage:' section."
-        type: "string"
-      namespace:
-        description: "Namespace this component is a part of. See the @[Namespaces\
-          \ guide](namespace) for more information on namespaces."
-        type: "string"
-      arguments:
-        description: "A list of @[arguments](argument) for this component. For each\
-          \ argument, a type and a name must be specified. Depending on the type of\
-          \ argument, different properties can be set. See these reference pages per\
-          \ type for more information:  \n\n - @[string](arg_string)\n - @[file](arg_file)\n\
-          \ - @[integer](arg_integer)\n - @[double](arg_double)\n - @[boolean](arg_boolean)\n\
-          \ - @[boolean_true](arg_boolean_true)\n - @[boolean_false](arg_boolean_false)\n"
-        type: "array"
-        items:
-          $ref: "#/definitions/Argument"
-    required:
-    - "name"
-    additionalProperties: false
-  Author:
-    description: "Author metadata."
-    type: "object"
-    properties:
-      name:
-        description: "Full name of the author, usually in the name of FirstName MiddleName\
-          \ LastName."
-        type: "string"
-      email:
-        description: "E-mail of the author."
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      roles:
-        anyOf:
-        - description: "Role of the author. Suggested items:\n\n* `\"author\"`: Authors\
-            \ who have made substantial contributions to the component.\n* `\"maintainer\"\
-            `: The maintainer of the component.\n* `\"contributor\"`: Authors who\
-            \ have made smaller contributions (such as code patches etc.).\n"
-          type: "string"
-        - description: "Role of the author. Suggested items:\n\n* `\"author\"`: Authors\
-            \ who have made substantial contributions to the component.\n* `\"maintainer\"\
-            `: The maintainer of the component.\n* `\"contributor\"`: Authors who\
-            \ have made smaller contributions (such as code patches etc.).\n"
-          type: "array"
-          items:
-            type: "string"
-      props:
-        description: "Author properties. Must be a map of strings."
-        type: "object"
-        additionalProperties:
-          description: "Author properties. Must be a map of strings."
-          type: "string"
-    required:
-    - "name"
-    additionalProperties: false
-  ComputationalRequirements:
-    description: "Computational requirements related to running the component."
-    type: "object"
-    properties:
-      cpus:
-        description: "The maximum number of (logical) cpus a component is allowed\
-          \ to use."
-        type: "integer"
-      commands:
-        description: "A list of commands which should be present on the system for\
-          \ the script to function."
-        type: "array"
-        items:
-          type: "string"
-      memory:
-        description: "The maximum amount of memory a component is allowed to allocate.\
-          \ Unit must be one of B, KB, MB, GB, TB or PB."
-        type: "string"
-    required: []
-    additionalProperties: false
-  RubyRequirements:
-    description: "Specify which Ruby packages should be available in order to run\
-      \ the component."
-    type: "object"
-    properties:
-      type:
-        description: "Specify which Ruby packages should be available in order to\
-          \ run the component."
-        const: "ruby"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install."
-          type: "string"
-        - description: "Specifies which packages to install."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  YumRequirements:
-    description: "Specify which yum packages should be available in order to run the\
-      \ component."
-    type: "object"
-    properties:
-      type:
-        description: "Specify which yum packages should be available in order to run\
-          \ the component."
-        const: "yum"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install."
-          type: "string"
-        - description: "Specifies which packages to install."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  JavascriptRequirements:
-    description: "Specify which JavaScript packages should be available in order to\
-      \ run the component."
-    type: "object"
-    properties:
-      github:
-        anyOf:
-        - description: "Specifies which packages to install from GitHub."
-          type: "string"
-        - description: "Specifies which packages to install from GitHub."
-          type: "array"
-          items:
-            type: "string"
-      url:
-        anyOf:
-        - description: "Specifies which packages to install using a generic URI."
-          type: "string"
-        - description: "Specifies which packages to install using a generic URI."
-          type: "array"
-          items:
-            type: "string"
-      git:
-        anyOf:
-        - description: "Specifies which packages to install using a Git URI."
-          type: "string"
-        - description: "Specifies which packages to install using a Git URI."
-          type: "array"
-          items:
-            type: "string"
-      npm:
-        anyOf:
-        - description: "Specifies which packages to install from npm."
-          type: "string"
-        - description: "Specifies which packages to install from npm."
-          type: "array"
-          items:
-            type: "string"
-      type:
-        description: "Specify which JavaScript packages should be available in order\
-          \ to run the component."
-        const: "javascript"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install from npm."
-          type: "string"
-        - description: "Specifies which packages to install from npm."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  DockerRequirements:
-    description: "Specify which Docker commands should be run during setup."
-    type: "object"
-    properties:
-      run:
-        anyOf:
-        - description: "Specifies which `RUN` entries to add to the Dockerfile while\
-            \ building it."
-          type: "string"
-        - description: "Specifies which `RUN` entries to add to the Dockerfile while\
-            \ building it."
-          type: "array"
-          items:
-            type: "string"
-      label:
-        anyOf:
-        - description: "Specifies which `LABEL` entries to add to the Dockerfile while\
-            \ building it."
-          type: "string"
-        - description: "Specifies which `LABEL` entries to add to the Dockerfile while\
-            \ building it."
-          type: "array"
-          items:
-            type: "string"
-      build_args:
-        anyOf:
-        - description: "Specifies which `ARG` entries to add to the Dockerfile while\
-            \ building it."
-          type: "string"
-        - description: "Specifies which `ARG` entries to add to the Dockerfile while\
-            \ building it."
-          type: "array"
-          items:
-            type: "string"
-      type:
-        description: "Specify which Docker commands should be run during setup."
-        const: "docker"
-      add:
-        anyOf:
-        - description: "Specifies which `ADD` entries to add to the Dockerfile while\
-            \ building it."
-          type: "string"
-        - description: "Specifies which `ADD` entries to add to the Dockerfile while\
-            \ building it."
-          type: "array"
-          items:
-            type: "string"
-      env:
-        anyOf:
-        - description: "Specifies which `ENV` entries to add to the Dockerfile while\
-            \ building it. Unlike `ARG`, `ENV` entries are also accessible from inside\
-            \ the container."
-          type: "string"
-        - description: "Specifies which `ENV` entries to add to the Dockerfile while\
-            \ building it. Unlike `ARG`, `ENV` entries are also accessible from inside\
-            \ the container."
-          type: "array"
-          items:
-            type: "string"
-      copy:
-        anyOf:
-        - description: "Specifies which `COPY` entries to add to the Dockerfile while\
-            \ building it."
-          type: "string"
-        - description: "Specifies which `COPY` entries to add to the Dockerfile while\
-            \ building it."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  RRequirements:
-    description: "Specify which R packages should be available in order to run the\
-      \ component."
-    type: "object"
-    properties:
-      bioc:
-        anyOf:
-        - description: "Specifies which packages to install from BioConductor."
-          type: "string"
-        - description: "Specifies which packages to install from BioConductor."
-          type: "array"
-          items:
-            type: "string"
-      github:
-        anyOf:
-        - description: "Specifies which packages to install from GitHub."
-          type: "string"
-        - description: "Specifies which packages to install from GitHub."
-          type: "array"
-          items:
-            type: "string"
-      gitlab:
-        anyOf:
-        - description: "Specifies which packages to install from GitLab."
-          type: "string"
-        - description: "Specifies which packages to install from GitLab."
-          type: "array"
-          items:
-            type: "string"
-      url:
-        anyOf:
-        - description: "Specifies which packages to install using a generic URI."
-          type: "string"
-        - description: "Specifies which packages to install using a generic URI."
-          type: "array"
-          items:
-            type: "string"
-      bioc_force_install:
-        description: "Forces packages specified in `bioc` to be reinstalled, even\
-          \ if they are already present in the container. Default: false."
-        type: "boolean"
-      git:
-        anyOf:
-        - description: "Specifies which packages to install using a Git URI."
-          type: "string"
-        - description: "Specifies which packages to install using a Git URI."
-          type: "array"
-          items:
-            type: "string"
-      cran:
-        anyOf:
-        - description: "Specifies which packages to install from CRAN."
-          type: "string"
-        - description: "Specifies which packages to install from CRAN."
-          type: "array"
-          items:
-            type: "string"
-      bitbucket:
-        anyOf:
-        - description: "Specifies which packages to install from Bitbucket."
-          type: "string"
-        - description: "Specifies which packages to install from Bitbucket."
-          type: "array"
-          items:
-            type: "string"
-      svn:
-        anyOf:
-        - description: "Specifies which packages to install using an SVN URI."
-          type: "string"
-        - description: "Specifies which packages to install using an SVN URI."
-          type: "array"
-          items:
-            type: "string"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install from CRAN."
-          type: "string"
-        - description: "Specifies which packages to install from CRAN."
-          type: "array"
-          items:
-            type: "string"
-      script:
-        anyOf:
-        - description: "Specifies a code block to run as part of the build."
-          type: "string"
-        - description: "Specifies a code block to run as part of the build."
-          type: "array"
-          items:
-            type: "string"
-      type:
-        description: "Specify which R packages should be available in order to run\
-          \ the component."
-        const: "r"
-    required:
-    - "type"
-    additionalProperties: false
-  ApkRequirements:
-    description: "Specify which apk packages should be available in order to run the\
-      \ component."
-    type: "object"
-    properties:
-      type:
-        description: "Specify which apk packages should be available in order to run\
-          \ the component."
-        const: "apk"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install."
-          type: "string"
-        - description: "Specifies which packages to install."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  PythonRequirements:
-    description: "Specify which Python packages should be available in order to run\
-      \ the component."
-    type: "object"
-    properties:
-      github:
-        anyOf:
-        - description: "Specifies which packages to install from GitHub."
-          type: "string"
-        - description: "Specifies which packages to install from GitHub."
-          type: "array"
-          items:
-            type: "string"
-      gitlab:
-        anyOf:
-        - description: "Specifies which packages to install from GitLab."
-          type: "string"
-        - description: "Specifies which packages to install from GitLab."
-          type: "array"
-          items:
-            type: "string"
-      pip:
-        anyOf:
-        - description: "Specifies which packages to install from pip."
-          type: "string"
-        - description: "Specifies which packages to install from pip."
-          type: "array"
-          items:
-            type: "string"
-      pypi:
-        anyOf:
-        - description: "Specifies which packages to install from PyPI using pip."
-          type: "string"
-        - description: "Specifies which packages to install from PyPI using pip."
-          type: "array"
-          items:
-            type: "string"
-      git:
-        anyOf:
-        - description: "Specifies which packages to install using a Git URI."
-          type: "string"
-        - description: "Specifies which packages to install using a Git URI."
-          type: "array"
-          items:
-            type: "string"
-      upgrade:
-        description: "Sets the `--upgrade` flag when set to true. Default: true."
-        type: "boolean"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install from pip."
-          type: "string"
-        - description: "Specifies which packages to install from pip."
-          type: "array"
-          items:
-            type: "string"
-      url:
-        anyOf:
-        - description: "Specifies which packages to install using a generic URI."
-          type: "string"
-        - description: "Specifies which packages to install using a generic URI."
-          type: "array"
-          items:
-            type: "string"
-      svn:
-        anyOf:
-        - description: "Specifies which packages to install using an SVN URI."
-          type: "string"
-        - description: "Specifies which packages to install using an SVN URI."
-          type: "array"
-          items:
-            type: "string"
-      bazaar:
-        anyOf:
-        - description: "Specifies which packages to install using a Bazaar URI."
-          type: "string"
-        - description: "Specifies which packages to install using a Bazaar URI."
-          type: "array"
-          items:
-            type: "string"
-      script:
-        anyOf:
-        - description: "Specifies a code block to run as part of the build."
-          type: "string"
-        - description: "Specifies a code block to run as part of the build."
-          type: "array"
-          items:
-            type: "string"
-      type:
-        description: "Specify which Python packages should be available in order to\
-          \ run the component."
-        const: "python"
-      mercurial:
-        anyOf:
-        - description: "Specifies which packages to install using a Mercurial URI."
-          type: "string"
-        - description: "Specifies which packages to install using a Mercurial URI."
-          type: "array"
-          items:
-            type: "string"
-      user:
-        description: "Sets the `--user` flag when set to true. Default: false."
-        type: "boolean"
-    required:
-    - "type"
-    additionalProperties: false
-  AptRequirements:
-    description: "Specify which apt packages should be available in order to run the\
-      \ component."
-    type: "object"
-    properties:
-      interactive:
-        description: "If `false`, the Debian frontend is set to non-interactive (recommended).\
-          \ Default: false."
-        type: "boolean"
-      type:
-        description: "Specify which apt packages should be available in order to run\
-          \ the component."
-        const: "apt"
-      packages:
-        anyOf:
-        - description: "Specifies which packages to install."
-          type: "string"
-        - description: "Specifies which packages to install."
-          type: "array"
-          items:
-            type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  Requirements:
-    anyOf:
-    - $ref: "#/definitions/RubyRequirements"
-    - $ref: "#/definitions/YumRequirements"
-    - $ref: "#/definitions/JavascriptRequirements"
-    - $ref: "#/definitions/DockerRequirements"
-    - $ref: "#/definitions/RRequirements"
-    - $ref: "#/definitions/ApkRequirements"
-    - $ref: "#/definitions/PythonRequirements"
-    - $ref: "#/definitions/AptRequirements"
-  StringArgument:
-    description: "A `string` type argument has a value made up of an ordered sequences\
-      \ of characters, like \"Hello\" or \"I'm a string\"."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f`\
-          \ or `foo`. The number of dashes determines how values can be passed:  \n\
-          \n  - `--foo` is a long option, which can be passed with `executable_name\
-          \ --foo=value` or `executable_name --foo value`\n  - `-f` is a short option,\
-          \ which can be passed with `executable_name -f value`\n  - `foo` is an argument,\
-          \ which can be passed with `executable_name value`  \n"
-        type: "string"
-      choices:
-        description: "Limit the amount of valid values for this argument to those\
-          \ set in this list. When set and a value not present in the list is provided,\
-          \ an error will be produced."
-        type: "array"
-        items:
-          type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "string"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "string"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "string"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "string"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "A `string` type argument has a value made up of an ordered sequences\
-          \ of characters, like \"Hello\" or \"I'm a string\"."
-        const: "string"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  BooleanArgument:
-    description: "A `boolean` type argument has two possible values: `true` or `false`."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--trim`, `-t`\
-          \ or `trim`. The number of dashes determines how values can be passed: \
-          \ \n\n  - `--trim` is a long option, which can be passed with `executable_name\
-          \ --trim`\n  - `-t` is a short option, which can be passed with `executable_name\
-          \ -t`\n  - `trim` is an argument, which can be passed with `executable_name\
-          \ trim`  \n"
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "boolean"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "boolean"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "boolean"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "boolean"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "A `boolean` type argument has two possible values: `true` or\
-          \ `false`."
-        const: "boolean"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  BooleanTrueArgument:
-    description: "An argument of the `boolean_true` type acts like a `boolean` flag\
-      \ with a default value of `false`. When called as an argument it sets the `boolean`\
-      \ to `true`."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--silent`,\
-          \ `-s` or `silent`. The number of dashes determines how values can be passed:\
-          \  \n\n  - `--silent` is a long option, which can be passed with `executable_name\
-          \ --silent`\n  - `-s` is a short option, which can be passed with `executable_name\
-          \ -s`\n  - `silent` is an argument, which can be passed with `executable_name\
-          \ silent`  \n"
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      type:
-        description: "An argument of the `boolean_true` type acts like a `boolean`\
-          \ flag with a default value of `false`. When called as an argument it sets\
-          \ the `boolean` to `true`."
-        const: "boolean_true"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  IntegerArgument:
-    description: "An `integer` type argument has a numeric value without decimal points."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f`\
-          \ or `foo`. The number of dashes determines how values can be passed:  \n\
-          \n  - `--foo` is a long option, which can be passed with `executable_name\
-          \ --foo=value` or `executable_name --foo value`\n  - `-f` is a short option,\
-          \ which can be passed with `executable_name -f value`\n  - `foo` is an argument,\
-          \ which can be passed with `executable_name value`  \n"
-        type: "string"
-      choices:
-        description: "Limit the amount of valid values for this argument to those\
-          \ set in this list. When set and a value not present in the list is provided,\
-          \ an error will be produced."
-        type: "array"
-        items:
-          type: "integer"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      max:
-        description: "Maximum allowed value for this argument. If set and the provided\
-          \ value is higher than the maximum, an error will be produced. Can be combined\
-          \ with [`min`](#min) to clamp values."
-        type: "integer"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "integer"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "integer"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "integer"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "integer"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      min:
-        description: "Minimum allowed value for this argument. If set and the provided\
-          \ value is lower than the minimum, an error will be produced. Can be combined\
-          \ with [`max`](#max) to clamp values."
-        type: "integer"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "An `integer` type argument has a numeric value without decimal\
-          \ points."
-        const: "integer"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  LongArgument:
-    description: "An `long` type argument has a numeric value without decimal points."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f`\
-          \ or `foo`. The number of dashes determines how values can be passed:  \n\
-          \n  - `--foo` is a long option, which can be passed with `executable_name\
-          \ --foo=value` or `executable_name --foo value`\n  - `-f` is a short option,\
-          \ which can be passed with `executable_name -f value`\n  - `foo` is an argument,\
-          \ which can be passed with `executable_name value`  \n"
-        type: "string"
-      choices:
-        description: "Limit the amount of valid values for this argument to those\
-          \ set in this list. When set and a value not present in the list is provided,\
-          \ an error will be produced."
-        type: "array"
-        items:
-          type: "integer"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      max:
-        description: "Maximum allowed value for this argument. If set and the provided\
-          \ value is higher than the maximum, an error will be produced. Can be combined\
-          \ with [`min`](#min) to clamp values."
-        type: "integer"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "integer"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "integer"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "integer"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "integer"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      min:
-        description: "Minimum allowed value for this argument. If set and the provided\
-          \ value is lower than the minimum, an error will be produced. Can be combined\
-          \ with [`max`](#max) to clamp values."
-        type: "integer"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "An `long` type argument has a numeric value without decimal\
-          \ points."
-        const: "long"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  BooleanFalseArgument:
-    description: "An argument of the `boolean_false` type acts like an inverted `boolean`\
-      \ flag with a default value of `true`. When called as an argument it sets the\
-      \ `boolean` to `false`."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--no-log`,\
-          \ `-n` or `no-log`. The number of dashes determines how values can be passed:\
-          \  \n\n  - `--no-log` is a long option, which can be passed with `executable_name\
-          \ --no-log`\n  - `-n` is a short option, which can be passed with `executable_name\
-          \ -n`\n  - `no-log` is an argument, which can be passed with `executable_name\
-          \ no-log`  \n"
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      type:
-        description: "An argument of the `boolean_false` type acts like an inverted\
-          \ `boolean` flag with a default value of `true`. When called as an argument\
-          \ it sets the `boolean` to `false`."
-        const: "boolean_false"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  DoubleArgument:
-    description: "A `double` type argument has a numeric value with decimal points"
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f`\
-          \ or `foo`. The number of dashes determines how values can be passed:  \n\
-          \n  - `--foo` is a long option, which can be passed with `executable_name\
-          \ --foo=value` or `executable_name --foo value`\n  - `-f` is a short option,\
-          \ which can be passed with `executable_name -f value`\n  - `foo` is an argument,\
-          \ which can be passed with `executable_name value`  \n"
-        type: "string"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      max:
-        description: "Maximum allowed value for this argument. If set and the provided\
-          \ value is higher than the maximum, an error will be produced. Can be combined\
-          \ with [`min`](#min) to clamp values."
-        type: "number"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "number"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "number"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "number"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "number"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      min:
-        description: "Minimum allowed value for this argument. If set and the provided\
-          \ value is lower than the minimum, an error will be produced. Can be combined\
-          \ with [`max`](#max) to clamp values."
-        type: "number"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "A `double` type argument has a numeric value with decimal points"
-        const: "double"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  FileArgument:
-    description: "A `file` type argument has a string value that points to a file\
-      \ or folder path."
-    type: "object"
-    properties:
-      alternatives:
-        anyOf:
-        - description: "List of alternative format variations for this argument."
-          type: "string"
-        - description: "List of alternative format variations for this argument."
-          type: "array"
-          items:
-            type: "string"
-      name:
-        description: "The name of the argument. Can be in the formats `--foo`, `-f`\
-          \ or `foo`. The number of dashes determines how values can be passed:  \n\
-          \n  - `--foo` is a long option, which can be passed with `executable_name\
-          \ --foo=value` or `executable_name --foo value`\n  - `-f` is a short option,\
-          \ which can be passed with `executable_name -f value`\n  - `foo` is an argument,\
-          \ which can be passed with `executable_name value`  \n"
-        type: "string"
-      create_parent:
-        description: "If the output filename is a path and it does not exist, create\
-          \ it before executing the script (only for `direction: output`)."
-        type: "boolean"
-      direction:
-        description: "Makes this argument an `input` or an `output`, as in does the\
-          \ file/folder needs to be read or written. `input` by default."
-        $ref: "#/definitions/Direction"
-      info:
-        description: "Structured information. Can be any shape: a string, vector,\
-          \ map or even nested map."
-        type: "object"
-      must_exist:
-        description: "Checks whether the file or folder exists. For input files, this\
-          \ check will happen before the execution of the script, while for output\
-          \ files the check will happen afterwards."
-        type: "boolean"
-      default:
-        anyOf:
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "string"
-        - description: "The default value when no argument value is provided. This\
-            \ will not work if the [`required`](#required) property is enabled."
-          type: "array"
-          items:
-            type: "string"
-      example:
-        anyOf:
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "string"
-        - description: "An example value for this argument. If no [`default`](#default)\
-            \ property was specified, this will be used for that purpose."
-          type: "array"
-          items:
-            type: "string"
-      description:
-        description: "A description of the argument. This will be displayed with `--help`."
-        type: "string"
-      multiple_sep:
-        description: "The delimiter character for providing [`multiple`](#multiple)\
-          \ values. `:` by default."
-        type: "string"
-      multiple:
-        description: "Treat the argument value as an array. Arrays can be passed using\
-          \ the delimiter `--foo=1:2:3` or by providing the same argument multiple\
-          \ times `--foo 1 --foo 2`. You can use a custom delimiter by using the [`multiple_sep`](#multiple_sep)\
-          \ property. `false` by default."
-        type: "boolean"
-      type:
-        description: "A `file` type argument has a string value that points to a file\
-          \ or folder path."
-        const: "file"
-      required:
-        description: "Make the value for this argument required. If set to `true`,\
-          \ an error will be produced if no value was provided. `false` by default."
-        type: "boolean"
-    required:
-    - "name"
-    - "type"
-    additionalProperties: false
-  Argument:
-    anyOf:
-    - $ref: "#/definitions/StringArgument"
-    - $ref: "#/definitions/BooleanArgument"
-    - $ref: "#/definitions/BooleanTrueArgument"
-    - $ref: "#/definitions/IntegerArgument"
-    - $ref: "#/definitions/LongArgument"
-    - $ref: "#/definitions/BooleanFalseArgument"
-    - $ref: "#/definitions/DoubleArgument"
-    - $ref: "#/definitions/FileArgument"
-  ArgumentGroup:
-    type: "object"
-    properties:
-      name:
-        description: "The name of the argument group."
-        type: "string"
-      description:
-        description: "A description of the argument group. Multiline descriptions\
-          \ are supported."
-        type: "string"
-      arguments:
-        description: "List of the arguments names."
-        type: "array"
-        items:
-          $ref: "#/definitions/Argument"
-    required:
-    - "name"
-    - "arguments"
-    additionalProperties: false
-  JavaScriptScript:
-    description: "An executable JavaScript script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable JavaScript script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "javascript_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  CSharpScript:
-    description: "An executable C# script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable C# script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "csharp_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  Executable:
-    description: "An executable file."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable file."
-        const: "executable"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  ScalaScript:
-    description: "An executable Scala script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable Scala script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "scala_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  NextflowScript:
-    description: "A Nextflow script. Work in progress; added mainly for annotation\
-      \ at the moment."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      entrypoint:
-        description: "The name of the workflow to be executed."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "A Nextflow script. Work in progress; added mainly for annotation\
-          \ at the moment."
-        const: "nextflow_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  PlainFile:
-    description: "A plain file. This can only be used as a supporting resource for\
-      \ the main script or unit tests."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "A plain file. This can only be used as a supporting resource\
-          \ for the main script or unit tests."
-        const: "file"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "path"
-    additionalProperties: false
-  BashScript:
-    description: "An executable Bash script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable Bash script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "bash_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  PythonScript:
-    description: "An executable Python script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable Python script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "python_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  RScript:
-    description: "An executable R script.\nWhen defined in functionality.resources,\
-      \ only the first entry will be executed when running the built component or\
-      \ when running `viash run`.\nWhen defined in functionality.test_resources, all\
-      \ entries will be executed during `viash test`."
-    type: "object"
-    properties:
-      path:
-        description: "The path of the input file. Can be a relative or an absolute\
-          \ path, or a URI. Mutually exclusive with `text`."
-        type: "string"
-      text:
-        description: "The content of the resulting file specified as a string. Mutually\
-          \ exclusive with `path`."
-        type: "string"
-      is_executable:
-        description: "Whether the resulting resource file should be made executable."
-        type: "boolean"
-      type:
-        description: "An executable R script.\nWhen defined in functionality.resources,\
-          \ only the first entry will be executed when running the built component\
-          \ or when running `viash run`.\nWhen defined in functionality.test_resources,\
-          \ all entries will be executed during `viash test`."
-        const: "r_script"
-      dest:
-        description: "Resulting filename of the resource. From within a script, the\
-          \ file can be accessed at `meta[\"resources_dir\"] + \"/\" + dest`. If unspecified,\
-          \ `dest` will be set to the basename of the `path` parameter."
-        type: "string"
-    required:
-    - "type"
-    additionalProperties: false
-  Resource:
-    anyOf:
-    - $ref: "#/definitions/JavaScriptScript"
-    - $ref: "#/definitions/CSharpScript"
-    - $ref: "#/definitions/Executable"
-    - $ref: "#/definitions/ScalaScript"
-    - $ref: "#/definitions/NextflowScript"
-    - $ref: "#/definitions/PlainFile"
-    - $ref: "#/definitions/BashScript"
-    - $ref: "#/definitions/PythonScript"
-    - $ref: "#/definitions/RScript"
-  NextflowDirectives:
-    description: "Directives are optional settings that affect the execution of the\
-      \ process.\n"
-    type: "object"
-    properties:
-      beforeScript:
-        description: "The `beforeScript` directive allows you to execute a custom\
-          \ (Bash) snippet before the main process script is run. This may be useful\
-          \ to initialise the underlying cluster environment or for other custom initialisation.\n\
-          \nSee [`beforeScript`](https://www.nextflow.io/docs/latest/process.html#beforeScript).\n"
-        type: "string"
-      module:
-        anyOf:
-        - description: "Environment Modules is a package manager that allows you to\
-            \ dynamically configure your execution environment and easily switch between\
-            \ multiple versions of the same software tool.\n\nIf it is available in\
-            \ your system you can use it with Nextflow in order to configure the processes\
-            \ execution environment in your pipeline.\n\nIn a process definition you\
-            \ can use the `module` directive to load a specific module version to\
-            \ be used in the process execution environment.\n\nSee [`module`](https://www.nextflow.io/docs/latest/process.html#module).\n"
-          type: "string"
-        - description: "Environment Modules is a package manager that allows you to\
-            \ dynamically configure your execution environment and easily switch between\
-            \ multiple versions of the same software tool.\n\nIf it is available in\
-            \ your system you can use it with Nextflow in order to configure the processes\
-            \ execution environment in your pipeline.\n\nIn a process definition you\
-            \ can use the `module` directive to load a specific module version to\
-            \ be used in the process execution environment.\n\nSee [`module`](https://www.nextflow.io/docs/latest/process.html#module).\n"
-          type: "array"
-          items:
-            type: "string"
-      queue:
-        anyOf:
-        - description: "The `queue` directory allows you to set the queue where jobs\
-            \ are scheduled when using a grid based executor in your pipeline.\n\n\
-            See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue).\n"
-          type: "string"
-        - description: "The `queue` directory allows you to set the queue where jobs\
-            \ are scheduled when using a grid based executor in your pipeline.\n\n\
-            See [`queue`](https://www.nextflow.io/docs/latest/process.html#queue).\n"
-          type: "array"
-          items:
-            type: "string"
-      label:
-        anyOf:
-        - description: "The `label` directive allows the annotation of processes with\
-            \ mnemonic identifier of your choice.\n\nSee [`label`](https://www.nextflow.io/docs/latest/process.html#label).\n"
-          type: "string"
-        - description: "The `label` directive allows the annotation of processes with\
-            \ mnemonic identifier of your choice.\n\nSee [`label`](https://www.nextflow.io/docs/latest/process.html#label).\n"
-          type: "array"
-          items:
-            type: "string"
-      container:
-        anyOf:
-        - description: "The `container` directive allows you to execute the process\
-            \ script in a Docker container.\n\nIt requires the Docker daemon to be\
-            \ running in machine where the pipeline is executed, i.e. the local machine\
-            \ when using the local executor or the cluster nodes when the pipeline\
-            \ is deployed through a grid executor.\n\nViash implements allows either\
-            \ a string value or a map. In case a map is used, the allowed keys are:\
-            \ `registry`, `image`, and `tag`. The `image` value must be specified.\n\
-            \nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n"
-          type: "object"
-          additionalProperties:
-            description: "The `container` directive allows you to execute the process\
-              \ script in a Docker container.\n\nIt requires the Docker daemon to\
-              \ be running in machine where the pipeline is executed, i.e. the local\
-              \ machine when using the local executor or the cluster nodes when the\
-              \ pipeline is deployed through a grid executor.\n\nViash implements\
-              \ allows either a string value or a map. In case a map is used, the\
-              \ allowed keys are: `registry`, `image`, and `tag`. The `image` value\
-              \ must be specified.\n\nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n"
-            type: "string"
-        - description: "The `container` directive allows you to execute the process\
-            \ script in a Docker container.\n\nIt requires the Docker daemon to be\
-            \ running in machine where the pipeline is executed, i.e. the local machine\
-            \ when using the local executor or the cluster nodes when the pipeline\
-            \ is deployed through a grid executor.\n\nViash implements allows either\
-            \ a string value or a map. In case a map is used, the allowed keys are:\
-            \ `registry`, `image`, and `tag`. The `image` value must be specified.\n\
-            \nSee [`container`](https://www.nextflow.io/docs/latest/process.html#container).\n"
-          type: "string"
-      publishDir:
-        anyOf:
-        - anyOf:
-          - description: "The `publishDir` directive allows you to publish the process\
-              \ output files to a specified folder.\n\nViash implements this directive\
-              \ as a plain string or a map. The allowed keywords for the map are:\
-              \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path`\
-              \ key and value are required.\nThe allowed values for `mode` are: `symlink`,\
-              \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-            type: "string"
-          - description: "The `publishDir` directive allows you to publish the process\
-              \ output files to a specified folder.\n\nViash implements this directive\
-              \ as a plain string or a map. The allowed keywords for the map are:\
-              \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path`\
-              \ key and value are required.\nThe allowed values for `mode` are: `symlink`,\
-              \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-            type: "object"
-            additionalProperties:
-              description: "The `publishDir` directive allows you to publish the process\
-                \ output files to a specified folder.\n\nViash implements this directive\
-                \ as a plain string or a map. The allowed keywords for the map are:\
-                \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\
-                \ `path` key and value are required.\nThe allowed values for `mode`\
-                \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\
-                \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-              type: "string"
-        - description: "The `publishDir` directive allows you to publish the process\
-            \ output files to a specified folder.\n\nViash implements this directive\
-            \ as a plain string or a map. The allowed keywords for the map are: `path`,\
-            \ `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The `path` key\
-            \ and value are required.\nThe allowed values for `mode` are: `symlink`,\
-            \ `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-          type: "array"
-          items:
-            anyOf:
-            - description: "The `publishDir` directive allows you to publish the process\
-                \ output files to a specified folder.\n\nViash implements this directive\
-                \ as a plain string or a map. The allowed keywords for the map are:\
-                \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\
-                \ `path` key and value are required.\nThe allowed values for `mode`\
-                \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\
-                \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-              type: "string"
-            - description: "The `publishDir` directive allows you to publish the process\
-                \ output files to a specified folder.\n\nViash implements this directive\
-                \ as a plain string or a map. The allowed keywords for the map are:\
-                \ `path`, `mode`, `overwrite`, `pattern`, `saveAs`, `enabled`. The\
-                \ `path` key and value are required.\nThe allowed values for `mode`\
-                \ are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.\n\
-                \nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-              type: "object"
-              additionalProperties:
-                description: "The `publishDir` directive allows you to publish the\
-                  \ process output files to a specified folder.\n\nViash implements\
-                  \ this directive as a plain string or a map. The allowed keywords\
-                  \ for the map are: `path`, `mode`, `overwrite`, `pattern`, `saveAs`,\
-                  \ `enabled`. The `path` key and value are required.\nThe allowed\
-                  \ values for `mode` are: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`,\
-                  \ `move`.\n\nSee [`publishDir`](https://www.nextflow.io/docs/latest/process.html#publishdir).\n"
-                type: "string"
-      maxForks:
-        anyOf:
-        - description: "The `maxForks` directive allows you to define the maximum\
-            \ number of process instances that can be executed in parallel. By default\
-            \ this value is equals to the number of CPU cores available minus 1.\n\
-            \nIf you want to execute a process in a sequential manner, set this directive\
-            \ to one.\n\nSee [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks).\n"
-          type: "string"
-        - description: "The `maxForks` directive allows you to define the maximum\
-            \ number of process instances that can be executed in parallel. By default\
-            \ this value is equals to the number of CPU cores available minus 1.\n\
-            \nIf you want to execute a process in a sequential manner, set this directive\
-            \ to one.\n\nSee [`maxForks`](https://www.nextflow.io/docs/latest/process.html#maxforks).\n"
-          type: "integer"
-      maxErrors:
-        anyOf:
-        - description: "The `maxErrors` directive allows you to specify the maximum\
-            \ number of times a process can fail when using the `retry` error strategy.\
-            \ By default this directive is disabled.\n\nSee [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors).\n"
-          type: "string"
-        - description: "The `maxErrors` directive allows you to specify the maximum\
-            \ number of times a process can fail when using the `retry` error strategy.\
-            \ By default this directive is disabled.\n\nSee [`maxErrors`](https://www.nextflow.io/docs/latest/process.html#maxerrors).\n"
-          type: "integer"
-      cpus:
-        anyOf:
-        - description: "The `cpus` directive allows you to define the number of (logical)\
-            \ CPU required by the process' task.\n\nSee [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus).\n"
-          type: "integer"
-        - description: "The `cpus` directive allows you to define the number of (logical)\
-            \ CPU required by the process' task.\n\nSee [`cpus`](https://www.nextflow.io/docs/latest/process.html#cpus).\n"
-          type: "string"
-      accelerator:
-        description: "The `accelerator` directive allows you to specify the hardware\
-          \ accelerator requirement for the task execution e.g. GPU processor.\n\n\
-          Viash implements this directive as a map with accepted keywords: `type`,\
-          \ `limit`, `request`, and `runtime`.\n\nSee [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator).\n"
-        type: "object"
-        additionalProperties:
-          description: "The `accelerator` directive allows you to specify the hardware\
-            \ accelerator requirement for the task execution e.g. GPU processor.\n\
-            \nViash implements this directive as a map with accepted keywords: `type`,\
-            \ `limit`, `request`, and `runtime`.\n\nSee [`accelerator`](https://www.nextflow.io/docs/latest/process.html#accelerator).\n"
-          type: "string"
-      time:
-        description: "The `time` directive allows you to define how long a process\
-          \ is allowed to run.\n\nSee [`time`](https://www.nextflow.io/docs/latest/process.html#time).\n"
-        type: "string"
-      afterScript:
-        description: "The `afterScript` directive allows you to execute a custom (Bash)\
-          \ snippet immediately after the main process has run. This may be useful\
-          \ to clean up your staging area.\n\nSee [`afterScript`](https://www.nextflow.io/docs/latest/process.html#afterscript).\n"
-        type: "string"
-      executor:
-        description: "The `executor` defines the underlying system where processes\
-          \ are executed. By default a process uses the executor defined globally\
-          \ in the nextflow.config file.\n\nThe `executor` directive allows you to\
-          \ configure what executor has to be used by the process, overriding the\
-          \ default configuration. The following values can be used:\n\n| Name | Executor\
-          \ |\n|------|----------|\n| awsbatch | The process is executed using the\
-          \ AWS Batch service. | \n| azurebatch | The process is executed using the\
-          \ Azure Batch service. | \n| condor | The process is executed using the\
-          \ HTCondor job scheduler. | \n| google-lifesciences | The process is executed\
-          \ using the Google Genomics Pipelines service. | \n| ignite | The process\
-          \ is executed using the Apache Ignite cluster. | \n| k8s | The process is\
-          \ executed using the Kubernetes cluster. | \n| local | The process is executed\
-          \ in the computer where Nextflow is launched. | \n| lsf | The process is\
-          \ executed using the Platform LSF job scheduler. | \n| moab | The process\
-          \ is executed using the Moab job scheduler. | \n| nqsii | The process is\
-          \ executed using the NQSII job scheduler. | \n| oge | Alias for the sge\
-          \ executor. | \n| pbs | The process is executed using the PBS/Torque job\
-          \ scheduler. | \n| pbspro | The process is executed using the PBS Pro job\
-          \ scheduler. | \n| sge | The process is executed using the Sun Grid Engine\
-          \ / Open Grid Engine. | \n| slurm | The process is executed using the SLURM\
-          \ job scheduler. | \n| tes | The process is executed using the GA4GH TES\
-          \ service. | \n| uge | Alias for the sge executor. |\n\nSee [`executor`](https://www.nextflow.io/docs/latest/process.html#executor).\n"
-        type: "string"
-      containerOptions:
-        anyOf:
-        - description: "The `containerOptions` directive allows you to specify any\
-            \ container execution option supported by the underlying container engine\
-            \ (ie. Docker, Singularity, etc). This can be useful to provide container\
-            \ settings only for a specific process e.g. mount a custom path.\n\nSee\
-            \ [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions).\n"
-          type: "string"
-        - description: "The `containerOptions` directive allows you to specify any\
-            \ container execution option supported by the underlying container engine\
-            \ (ie. Docker, Singularity, etc). This can be useful to provide container\
-            \ settings only for a specific process e.g. mount a custom path.\n\nSee\
-            \ [`containerOptions`](https://www.nextflow.io/docs/latest/process.html#containeroptions).\n"
-          type: "array"
-          items:
-            type: "string"
-      disk:
-        description: "The `disk` directive allows you to define how much local disk\
-          \ storage the process is allowed to use.\n\nSee [`disk`](https://www.nextflow.io/docs/latest/process.html#disk).\n"
-        type: "string"
-      tag:
-        description: "The `tag` directive allows you to associate each process execution\
-          \ with a custom label, so that it will be easier to identify them in the\
-          \ log file or in the trace execution report.\n\nSee [`tag`](https://www.nextflow.io/docs/latest/process.html#tag).\n"
-        type: "string"
-      conda:
-        anyOf:
-        - description: "The `conda` directive allows for the definition of the process\
-            \ dependencies using the Conda package manager.\n\nNextflow automatically\
-            \ sets up an environment for the given package names listed by in the\
-            \ `conda` directive.\n\nSee [`conda`](https://www.nextflow.io/docs/latest/process.html#conda).\n"
-          type: "string"
-        - description: "The `conda` directive allows for the definition of the process\
-            \ dependencies using the Conda package manager.\n\nNextflow automatically\
-            \ sets up an environment for the given package names listed by in the\
-            \ `conda` directive.\n\nSee [`conda`](https://www.nextflow.io/docs/latest/process.html#conda).\n"
-          type: "array"
-          items:
-            type: "string"
-      machineType:
-        description: " The `machineType` can be used to specify a predefined Google\
-          \ Compute Platform machine type when running using the Google Life Sciences\
-          \ executor.\n\nSee [`machineType`](https://www.nextflow.io/docs/latest/process.html#machinetype).\n"
-        type: "string"
-      stageInMode:
-        description: "The `stageInMode` directive defines how input files are staged-in\
-          \ to the process work directory. The following values are allowed:\n\n|\
-          \ Value | Description |\n|-------|-------------| \n| copy | Input files\
-          \ are staged in the process work directory by creating a copy. | \n| link\
-          \ | Input files are staged in the process work directory by creating an\
-          \ (hard) link for each of them. | \n| symlink | Input files are staged in\
-          \ the process work directory by creating a symbolic link with an absolute\
-          \ path for each of them (default). | \n| rellink | Input files are staged\
-          \ in the process work directory by creating a symbolic link with a relative\
-          \ path for each of them. | \n\nSee [`stageInMode`](https://www.nextflow.io/docs/latest/process.html#stageinmode).\n"
-        type: "string"
-      cache:
-        anyOf:
-        - description: "The `cache` directive allows you to store the process results\
-            \ to a local cache. When the cache is enabled and the pipeline is launched\
-            \ with the resume option, any following attempt to execute the process,\
-            \ along with the same inputs, will cause the process execution to be skipped,\
-            \ producing the stored data as the actual results.\n\nThe caching feature\
-            \ generates a unique key by indexing the process script and inputs. This\
-            \ key is used to identify univocally the outputs produced by the process\
-            \ execution.\n\nThe `cache` is enabled by default, you can disable it\
-            \ for a specific process by setting the cache directive to `false`.\n\n\
-            Accepted values are: `true`, `false`, `\"deep\"`, and `\"lenient\"`.\n\
-            \nSee [`cache`](https://www.nextflow.io/docs/latest/process.html#cache).\n"
-          type: "boolean"
-        - description: "The `cache` directive allows you to store the process results\
-            \ to a local cache. When the cache is enabled and the pipeline is launched\
-            \ with the resume option, any following attempt to execute the process,\
-            \ along with the same inputs, will cause the process execution to be skipped,\
-            \ producing the stored data as the actual results.\n\nThe caching feature\
-            \ generates a unique key by indexing the process script and inputs. This\
-            \ key is used to identify univocally the outputs produced by the process\
-            \ execution.\n\nThe `cache` is enabled by default, you can disable it\
-            \ for a specific process by setting the cache directive to `false`.\n\n\
-            Accepted values are: `true`, `false`, `\"deep\"`, and `\"lenient\"`.\n\
-            \nSee [`cache`](https://www.nextflow.io/docs/latest/process.html#cache).\n"
-          type: "string"
-      pod:
-        anyOf:
-        - description: "The `pod` directive allows the definition of pods specific\
-            \ settings, such as environment variables, secrets and config maps when\
-            \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n"
-          type: "object"
-          additionalProperties:
-            description: "The `pod` directive allows the definition of pods specific\
-              \ settings, such as environment variables, secrets and config maps when\
-              \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n"
-            type: "string"
-        - description: "The `pod` directive allows the definition of pods specific\
-            \ settings, such as environment variables, secrets and config maps when\
-            \ using the Kubernetes executor.\n\nSee [`pod`](https://www.nextflow.io/docs/latest/process.html#pod).\n"
-          type: "array"
-          items:
-            type: "object"
-            additionalProperties:
-              type: "string"
-      penv:
-        description: "The `penv` directive allows you to define the parallel environment\
-          \ to be used when submitting a parallel task to the SGE resource manager.\n\
-          \nSee [`penv`](https://www.nextflow.io/docs/latest/process.html#penv).\n"
-        type: "string"
-      scratch:
-        anyOf:
-        - description: "The `scratch` directive allows you to execute the process\
-            \ in a temporary folder that is local to the execution node.\n\nSee [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch).\n"
-          type: "boolean"
-        - description: "The `scratch` directive allows you to execute the process\
-            \ in a temporary folder that is local to the execution node.\n\nSee [`scratch`](https://www.nextflow.io/docs/latest/process.html#scratch).\n"
-          type: "string"
-      storeDir:
-        description: "The `storeDir` directive allows you to define a directory that\
-          \ is used as a permanent cache for your process results.\n\nSee [`storeDir`](https://www.nextflow.io/docs/latest/process.html#storeDir).\n"
-        type: "string"
-      maxRetries:
-        anyOf:
-        - description: "The `maxRetries` directive allows you to define the maximum\
-            \ number of times a process instance can be re-submitted in case of failure.\
-            \ This value is applied only when using the retry error strategy. By default\
-            \ only one retry is allowed.\n\nSee [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries).\n"
-          type: "string"
-        - description: "The `maxRetries` directive allows you to define the maximum\
-            \ number of times a process instance can be re-submitted in case of failure.\
-            \ This value is applied only when using the retry error strategy. By default\
-            \ only one retry is allowed.\n\nSee [`maxRetries`](https://www.nextflow.io/docs/latest/process.html#maxretries).\n"
-          type: "integer"
-      echo:
-        anyOf:
-        - description: "By default the stdout produced by the commands executed in\
-            \ all processes is ignored. By setting the `echo` directive to true, you\
-            \ can forward the process stdout to the current top running process stdout\
-            \ file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n"
-          type: "boolean"
-        - description: "By default the stdout produced by the commands executed in\
-            \ all processes is ignored. By setting the `echo` directive to true, you\
-            \ can forward the process stdout to the current top running process stdout\
-            \ file, showing it in the shell terminal.\n \nSee [`echo`](https://www.nextflow.io/docs/latest/process.html#echo).\n"
-          type: "string"
-      errorStrategy:
-        description: "The `errorStrategy` directive allows you to define how an error\
-          \ condition is managed by the process. By default when an error status is\
-          \ returned by the executed script, the process stops immediately. This in\
-          \ turn forces the entire pipeline to terminate.\n\nTable of available error\
-          \ strategies:\n| Name | Executor |\n|------|----------|\n| `terminate` |\
-          \ Terminates the execution as soon as an error condition is reported. Pending\
-          \ jobs are killed (default) |\n| `finish` | Initiates an orderly pipeline\
-          \ shutdown when an error condition is raised, waiting the completion of\
-          \ any submitted job. |\n| `ignore` | Ignores processes execution errors.\
-          \ |\n| `retry` | Re-submit for execution a process returning an error condition.\
-          \ |\n\nSee [`errorStrategy`](https://www.nextflow.io/docs/latest/process.html#errorstrategy).\n"
-        type: "string"
-      memory:
-        description: "The `memory` directive allows you to define how much memory\
-          \ the process is allowed to use.\n\nSee [`memory`](https://www.nextflow.io/docs/latest/process.html#memory).\n"
-        type: "string"
-      stageOutMode:
-        description: "The `stageOutMode` directive defines how output files are staged-out\
-          \ from the scratch directory to the process work directory. The following\
-          \ values are allowed:\n\n| Value | Description |\n|-------|-------------|\
-          \ \n| copy | Output files are copied from the scratch directory to the work\
-          \ directory. | \n| move | Output files are moved from the scratch directory\
-          \ to the work directory. | \n| rsync | Output files are copied from the\
-          \ scratch directory to the work directory by using the rsync utility. |\n\
-          \nSee [`stageOutMode`](https://www.nextflow.io/docs/latest/process.html#stageoutmode).\n"
-        type: "string"
-    required: []
-    additionalProperties: false
-  NextflowAuto:
-    description: "Automated processing flags which can be toggled on or off."
-    type: "object"
-    properties:
-      simplifyInput:
-        description: "If `true`, an input tuple only containing only a single File\
-          \ (e.g. `[\"foo\", file(\"in.h5ad\")]`) is automatically transformed to\
-          \ a map (i.e. `[\"foo\", [ input: file(\"in.h5ad\") ] ]`).\n\nDefault: `true`.\n"
-        type: "boolean"
-      simplifyOutput:
-        description: "If `true`, an output tuple containing a map with a File (e.g.\
-          \ `[\"foo\", [ output: file(\"out.h5ad\") ] ]`) is automatically transformed\
-          \ to a map (i.e. `[\"foo\", file(\"out.h5ad\")]`).\n\nDefault: `true`.\n"
-        type: "boolean"
-      publish:
-        description: "If `true`, the module's outputs are automatically published\
-          \ to `params.publishDir`.\nWill throw an error if `params.publishDir` is\
-          \ not defined.\n\nDefault: `false`.\n"
-        type: "boolean"
-      transcript:
-        description: "If `true`, the module's transcripts from `work/` are automatically\
-          \ published to `params.transcriptDir`.\nIf not defined, `params.publishDir\
-          \ + \"/_transcripts\"` will be used.\nWill throw an error if neither are\
-          \ defined.\n\nDefault: `false`.\n"
-        type: "boolean"
-    required: []
-    additionalProperties: false
-  NextflowConfig:
-    description: "Allows tweaking how the Nextflow Config file is generated."
-    type: "object"
-    properties:
-      labels:
-        description: "A series of default labels to specify memory and cpu constraints.\n\
-          \nThe default memory labels are defined as \"mem1gb\", \"mem2gb\", \"mem4gb\"\
-          , ... upto \"mem512tb\" and follows powers of 2.\nThe default cpu labels\
-          \ are defined as \"cpu1\", \"cpu2\", \"cpu5\", \"cpu10\", ... upto \"cpu1000\"\
-          \ and follows a semi logarithmic scale (1, 2, 5 per decade).\n\nConceptually\
-          \ it is possible for a Viash Config to overwrite the full labels parameter,\
-          \ however likely it is more efficient to add additional labels\nin the Viash\
-          \ Project with a config mod.\n"
-        type: "object"
-        additionalProperties:
-          description: "A series of default labels to specify memory and cpu constraints.\n\
-            \nThe default memory labels are defined as \"mem1gb\", \"mem2gb\", \"\
-            mem4gb\", ... upto \"mem512tb\" and follows powers of 2.\nThe default\
-            \ cpu labels are defined as \"cpu1\", \"cpu2\", \"cpu5\", \"cpu10\", ...\
-            \ upto \"cpu1000\" and follows a semi logarithmic scale (1, 2, 5 per decade).\n\
-            \nConceptually it is possible for a Viash Config to overwrite the full\
-            \ labels parameter, however likely it is more efficient to add additional\
-            \ labels\nin the Viash Project with a config mod.\n"
-          type: "string"
-      script:
-        anyOf:
-        - description: "Includes a single string or list of strings into the nextflow.config\
-            \ file.\nThis can be used to add custom profiles or include an additional\
-            \ config file.\n"
-          type: "string"
-        - description: "Includes a single string or list of strings into the nextflow.config\
-            \ file.\nThis can be used to add custom profiles or include an additional\
-            \ config file.\n"
-          type: "array"
-          items:
-            type: "string"
-    required: []
-    additionalProperties: false
-  DockerSetupStrategy:
-    $comment: "TODO add descriptions to different strategies"
-    enum:
-    - "cb"
-    - "ifneedbepullelsecachedbuild"
-    - "donothing"
-    - "gentlepush"
-    - "alwayspullelsebuild"
-    - "build"
-    - "alwayspull"
-    - "alwaysbuild"
-    - "ifneedbebuild"
-    - "pullelsebuild"
-    - "p"
-    - "alwayspullelsecachedbuild"
-    - "pull"
-    - "maybepush"
-    - "ifneedbepullelsebuild"
-    - "cachedbuild"
-    - "pullelsecachedbuild"
-    - "push"
-    - "forcepush"
-    - "alwayspush"
-    - "b"
-    - "pushifnotpresent"
-    - "alwayscachedbuild"
-    - "meh"
-    - "ifneedbepull"
-    - "ifneedbecachedbuild"
-    description: "The Docker setup strategy to use when building a container."
-  Direction:
-    enum:
-    - "input"
-    - "output"
-    description: "Makes this argument an `input` or an `output`, as in does the file/folder\
-      \ needs to be read or written. `input` by default."
-  Status:
-    enum:
-    - "enabled"
-    - "disabled"
-    - "deprecated"
-    description: "Allows setting a component to active, deprecated or disabled."
-  DockerResolveVolume:
-    $comment: "TODO make fully case insensitive"
-    enum:
-    - "manual"
-    - "automatic"
-    - "auto"
-    - "Manual"
-    - "Automatic"
-    - "Auto"
-    description: "Enables or disables automatic volume mapping. Enabled when set to\
-      \ `Automatic` or disabled when set to `Manual`. Default: `Automatic`"
diff --git a/src/common/schemas/task_control_method.yaml b/src/common/schemas/task_control_method.yaml
deleted file mode 100644
index 8d62f6be43..0000000000
--- a/src/common/schemas/task_control_method.yaml
+++ /dev/null
@@ -1,68 +0,0 @@
-title: Control Method
-description: |
-  A control method is used to test the relative performance of all other methods,
-  and also as a quality control for the pipeline as a whole. A control method can
-  either be a positive control or a negative control. The positive control and
-  negative control methods set a maximum and minimum threshold for performance,
-  so any new method should perform better than the negative control methods and
-  worse than the positive control method.
-type: object
-required: [__merge__, functionality, platforms]
-properties:
-  __merge__:
-    "$ref": "defs_common.yaml#/definitions/CompAPIMerge"
-  functionality:
-    type: object
-    description: Information regarding the functionality of the component.
-    required: [name, info, resources]
-    additionalProperties: false
-    properties:
-      name:
-        "$ref": "defs_common.yaml#/definitions/Name"
-      status:
-        "$ref": "defs_viash.yaml#/definitions/Status"
-      info:
-        type: object
-        description: Metadata of the component.
-        additionalProperties: false
-        required: [label, summary, description, preferred_normalization]
-        properties:
-          label:
-            "$ref": "defs_common.yaml#/definitions/Label"
-          summary:
-            "$ref": "defs_common.yaml#/definitions/Summary"
-          description:
-            "$ref": "defs_common.yaml#/definitions/Description"
-          preferred_normalization: 
-            "$ref": "defs_common.yaml#/definitions/PreferredNormalization"
-          reference:
-            "$ref": "defs_common.yaml#/definitions/BibtexReference"
-          documentation_url:
-            "$ref": "defs_common.yaml#/definitions/DocumentationURL"
-          repository_url:
-            "$ref": "defs_common.yaml#/definitions/RepositoryURL"
-          variants:
-            "$ref": "defs_common.yaml#/definitions/MethodVariants"
-      arguments:
-        type: array
-        description: Component-specific parameters.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Argument"
-      resources:
-        type: array
-        description: Resources required to run the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-      test_resources:
-        type: array
-        description: One or more scripts and resources used to test the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-  platforms:
-    type: array
-    description: A list of platforms which Viash generates target artifacts for.
-    items:
-      anyOf:
-        - "$ref": "defs_common.yaml#/definitions/PlatformDocker"
-        - "$ref": "defs_common.yaml#/definitions/PlatformNative"
-        - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3"
diff --git a/src/common/schemas/task_info.yaml b/src/common/schemas/task_info.yaml
deleted file mode 100644
index be6a1e3447..0000000000
--- a/src/common/schemas/task_info.yaml
+++ /dev/null
@@ -1,22 +0,0 @@
-title: Task info
-description: A file format specification file.
-type: object
-additionalProperties: false
-required: [name, label, summary, motivation, description]
-properties:
-  name:
-    $ref: "defs_common.yaml#/definitions/Name"
-  label:
-    $ref: "defs_common.yaml#/definitions/Label"
-  summary: 
-    $ref: "defs_common.yaml#/definitions/Summary"
-  image:
-    $ref: "defs_common.yaml#/definitions/Image"
-  motivation: 
-    $ref: "defs_common.yaml#/definitions/Description"
-  description: 
-    $ref: "defs_common.yaml#/definitions/Description"
-  authors:
-    type: array
-    items:
-      $ref: "defs_common.yaml#/definitions/Author"
diff --git a/src/common/schemas/task_method.yaml b/src/common/schemas/task_method.yaml
deleted file mode 100644
index 25c59c7a47..0000000000
--- a/src/common/schemas/task_method.yaml
+++ /dev/null
@@ -1,65 +0,0 @@
-title: Method
-description: |
-  A method is a specific technique used to solve the task problem and is
-  compared to the control methods and other methods to determine the best
-  approach for the task depending on the type of dataset.
-type: object
-required: [__merge__, functionality, platforms]
-properties:
-  __merge__:
-    "$ref": "defs_common.yaml#/definitions/CompAPIMerge"
-  functionality:
-    type: object
-    description: Information regarding the functionality of the component.
-    required: [name, info, resources]
-    additionalProperties: false
-    properties:
-      name:
-        "$ref": "defs_common.yaml#/definitions/Name"
-      status:
-        "$ref": "defs_viash.yaml#/definitions/Status"
-      info:
-        type: object
-        description: Metadata of the component.
-        additionalProperties: false
-        required: [label, summary, description, preferred_normalization, reference, documentation_url, repository_url]
-        properties:
-          label:
-            "$ref": "defs_common.yaml#/definitions/Label"
-          summary:
-            "$ref": "defs_common.yaml#/definitions/Summary"
-          description:
-            "$ref": "defs_common.yaml#/definitions/Description"
-          preferred_normalization: 
-            "$ref": "defs_common.yaml#/definitions/PreferredNormalization"
-          reference:
-            "$ref": "defs_common.yaml#/definitions/BibtexReference"
-          documentation_url:
-            "$ref": "defs_common.yaml#/definitions/DocumentationURL"
-          repository_url:
-            "$ref": "defs_common.yaml#/definitions/RepositoryURL"
-          variants:
-            "$ref": "defs_common.yaml#/definitions/MethodVariants"
-      arguments:
-        type: array
-        description: Component-specific parameters.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Argument"
-      resources:
-        type: array
-        description: Resources required to run the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-      test_resources:
-        type: array
-        description: One or more scripts and resources used to test the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-  platforms:
-    type: array
-    description: A list of platforms which Viash generates target artifacts for.
-    items:
-      anyOf:
-        - "$ref": "defs_common.yaml#/definitions/PlatformDocker"
-        - "$ref": "defs_common.yaml#/definitions/PlatformNative"
-        - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3"
diff --git a/src/common/schemas/task_metric.yaml b/src/common/schemas/task_metric.yaml
deleted file mode 100644
index 35932e9e7a..0000000000
--- a/src/common/schemas/task_metric.yaml
+++ /dev/null
@@ -1,86 +0,0 @@
-title: Metric
-description: |
-  A metric is a quantitative measure used to evaluate the performance of the
-  different methods in solving the specific task problem.
-type: object
-required: [__merge__, functionality, platforms]
-properties:
-  __merge__:
-    "$ref": "defs_common.yaml#/definitions/CompAPIMerge"
-  functionality:
-    type: object
-    description: Information regarding the functionality of the component.
-    required: [name, info, resources]
-    additionalProperties: false
-    properties:
-      name:
-        "$ref": "defs_common.yaml#/definitions/Name"
-      status:
-        "$ref": "defs_viash.yaml#/definitions/Status"
-      info:
-        type: object
-        description: Metadata of the component.
-        additionalProperties: false
-        required: [metrics]
-        properties:
-          metrics:
-            type: array
-            minItems: 1
-            items:
-              type: object
-              description: Metadata of each metric.
-              additionalProperties: false
-              required: [label, summary, description, reference, min, max, maximize]
-              properties:
-                name:
-                  "$ref": "defs_common.yaml#/definitions/Name"
-                label:
-                  "$ref": "defs_common.yaml#/definitions/Label"
-                summary:
-                  "$ref": "defs_common.yaml#/definitions/Summary"
-                description:
-                  "$ref": "defs_common.yaml#/definitions/Description"
-                reference:
-                  "$ref": "defs_common.yaml#/definitions/BibtexReference"
-                documentation_url:
-                  "$ref": "defs_common.yaml#/definitions/DocumentationURL"
-                repository_url:
-                  "$ref": "defs_common.yaml#/definitions/RepositoryURL"
-                variants:
-                  "$ref": "defs_common.yaml#/definitions/MethodVariants"
-                min:
-                  description: The lowest possible value of the metric.
-                  oneOf:
-                    - type: number
-                    - const: "-.inf"
-                max:
-                  description: The highest possible value of the metric.
-                  oneOf:
-                    - type: number
-                    - const: "+.inf"
-                maximize:
-                  type: boolean
-                  description: Whether a higher metric value is better.
-      arguments:
-        type: array
-        description: Component-specific parameters.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Argument"
-      resources:
-        type: array
-        description: Resources required to run the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-      test_resources:
-        type: array
-        description: One or more scripts and resources used to test the component.
-        items:
-          "$ref": "defs_viash.yaml#/definitions/Resource"
-  platforms:
-    type: array
-    description: A list of platforms which Viash generates target artifacts for.
-    items:
-      anyOf:
-        - "$ref": "defs_common.yaml#/definitions/PlatformDocker"
-        - "$ref": "defs_common.yaml#/definitions/PlatformNative"
-        - "$ref": "defs_common.yaml#/definitions/PlatformVdsl3"