Update nf-core/tools API docs for dev

sites/docs/src/content/api_reference/dev/module_lint_tests/environment_yml.md

@@ -10,18 +10,35 @@ is sorted alphabetically.
 
 The following checks are performed:
 
-- `environment_yml_exists`: The `environment.yml` file must exist, unless the
-  module has a Dockerfile. If neither `environment.yml` nor a Dockerfile is
-  present, the test fails.
-- `environment_yml_dockerfile_conflict`: A module must not have both an
-  `environment.yml` and a Dockerfile; Remove the Dockerfile if present.
-- `environment_yml_valid`: The `environment.yml` must be valid according to
-  the JSON schema defined at <https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json>.
-- `environment_yml_sorted`: The dependencies listed in `environment.yml`
-  must be sorted alphabetically. If they are not, they will be sorted
-  automatically.
-- `bioconda_version`: The version specified for each bioconda package must
-  be a valid, known version available in the bioconda channel.
-- `bioconda_latest`: Each bioconda package should be pinned to the latest
-  available version. A warning is raised (or the version updated if
-  `fix_version` is set) when a newer version exists.
+## environment\_yml\_exists
+
+The `environment.yml` file must exist, unless the
+module has a Dockerfile. If neither `environment.yml` nor a Dockerfile is
+present, the test fails.
+
+## environment\_yml\_dockerfile\_conflict
+
+A module must not have both an
+`environment.yml` and a Dockerfile; Remove the Dockerfile if present.
+
+## environment\_yml\_valid
+
+The `environment.yml` must be valid according to
+the JSON schema defined at <https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json>.
+
+## environment\_yml\_sorted
+
+The dependencies listed in `environment.yml`
+must be sorted alphabetically. If they are not, they will be sorted
+automatically.
+
+## bioconda\_version
+
+The version specified for each bioconda package must
+be a valid, known version available in the bioconda channel.
+
+## bioconda\_latest
+
+Each bioconda package should be pinned to the latest
+available version. A warning is raised (or the version updated if
+`fix_version` is set) when a newer version exists.

sites/docs/src/content/api_reference/dev/module_lint_tests/main_nf.md

@@ -9,36 +9,71 @@ in which case failures will be reported as warnings.
 
 The following checks are performed:
 
-- `main_nf_module_granularity`: The module must represent a single command
-  as `<tool>` or single subcommand with distinct functionality as
-  `<tool/subtool>`.
-- `main_nf_exists`: The `main.nf` file must exist.
-- `deprecated_dsl2`: The file must not contain deprecated DSL2 identifiers
-  (`initOptions`, `saveFiles`, `getSoftwareName`, `getProcessName`,
-  `publishDir`).
-- `main_nf_script_outputs`: The process must have an `output:` block.
-- `main_nf_container`: When both a `singularity` and a `docker` container
-  are specified, their tags must reference the same software version. A warning
-  is issued if they do not match. Modules using the newer docker-only format
-  (no singularity container) skip this check.
-- `singularity_tag`: A Singularity container must be resolvable via
-  `nextflow inspect -profile singularity`. The check fails if none can be
-  resolved or if it falls back to a docker container that has an automatic
-  singularity equivalent, i.e., `quay.io/biocontainers/` or
-  `community.wave.seqera.io/`.
-  It is skipped for modules listed under `singularity` in `.github/skip_nf_test.json`.
-- `oras_singularity_tag`: The resolved Singularity container must not be
-  served over the `oras://` scheme; it should be a plain `https://` URL.
-  The check fails if an `oras://` container is used.
-- `main_nf_script_shell`: Exactly one of `script:`, `shell:`, or `exec:`
-  blocks must be present.
-- `main_nf_shell_template`: If a `shell:` block is used, it must call
-  a `template`.
-- `main_nf_meta_output`: If `meta` is present in the module inputs, it
-  must also appear in at least one output channel.
-- `main_nf_version_topic`: The module should emit software versions using
-  a `topic: versions` output. A warning is issued if no such topic is found.
-- `main_nf_version_emit`: The number of `topic: versions` outputs must
-  equal the number of `emit:` outputs whose name starts with `versions`.
-  A warning is issued if a legacy YAML-based `versions` emit is used instead
-  of a topic output.
+## main\_nf\_module\_granularity
+
+The module must represent a single command
+as `<tool>` or single subcommand with distinct functionality as
+`<tool/subtool>`.
+
+## main\_nf\_exists
+
+The `main.nf` file must exist.
+
+## deprecated\_dsl2
+
+The file must not contain deprecated DSL2 identifiers
+(`initOptions`, `saveFiles`, `getSoftwareName`, `getProcessName`,
+`publishDir`).
+
+## main\_nf\_script\_outputs
+
+The process must have an `output:` block.
+
+## main\_nf\_container
+
+When both a `singularity` and a `docker` container
+are specified, their tags must reference the same software version. A warning
+is issued if they do not match. Modules using the newer docker-only format
+(no singularity container) skip this check.
+
+## singularity\_tag
+
+A Singularity container must be resolvable via
+`nextflow inspect -profile singularity`. The check fails if none can be
+resolved or if it falls back to a docker container that has an automatic
+singularity equivalent, i.e., `quay.io/biocontainers/` or
+`community.wave.seqera.io/`.
+It is skipped for modules listed under `singularity` in `.github/skip_nf_test.json`.
+
+## oras\_singularity\_tag
+
+The resolved Singularity container must not be
+served over the `oras://` scheme; it should be a plain `https://` URL.
+The check fails if an `oras://` container is used.
+
+## main\_nf\_script\_shell
+
+Exactly one of `script:`, `shell:`, or `exec:`
+blocks must be present.
+
+## main\_nf\_shell\_template
+
+If a `shell:` block is used, it must call
+a `template`.
+
+## main\_nf\_meta\_output
+
+If `meta` is present in the module inputs, it
+must also appear in at least one output channel.
+
+## main\_nf\_version\_topic
+
+The module should emit software versions using
+a `topic: versions` output. A warning is issued if no such topic is found.
+
+## main\_nf\_version\_emit
+
+The number of `topic: versions` outputs must
+equal the number of `emit:` outputs whose name starts with `versions`.
+A warning is issued if a legacy YAML-based `versions` emit is used instead
+of a topic output.

sites/docs/src/content/api_reference/dev/module_lint_tests/meta_yml.md

@@ -10,34 +10,66 @@ to the nf-core JSON schema, and that its contents are consistent with
 
 The following checks are performed:
 
-- `meta_yml_exists`: The `meta.yml` file must exist.
-- `meta_yml_valid`: The `meta.yml` must be valid according to the JSON
-  schema defined in `modules/meta-schema.json` in the nf-core/modules
-  repository.
-- `meta_name`: The `name` field in `meta.yml` must match (case-insensitive)
-  the process name declared in `main.nf`.
-- `meta_input`: If `main.nf` declares inputs, they must be listed under
-  the `input:` key in `meta.yml`.
-- `correct_meta_inputs`: The inputs listed in `meta.yml` must exactly
-  match those parsed from `main.nf`. Run `nf-core modules lint --fix`
-  to auto-correct.
-- `meta_output`: If `main.nf` declares outputs, they must be listed under
-  the `output:` key in `meta.yml`.
-- `correct_meta_outputs`: The outputs listed in `meta.yml` must exactly
-  match those parsed from `main.nf`. Run `nf-core modules lint --fix`
-  to auto-correct.
-- `has_meta_topics`: If `main.nf` declares topics, `meta.yml` must
-  also contain a non-empty `topics:` block. Run
-  `nf-core modules lint --fix` to auto-correct.
-- `correct_meta_topics`: The topics listed in `meta.yml` must exactly
-  match those parsed from `main.nf`. Run `nf-core modules lint --fix`
-  to auto-correct.
-- `has_meta_containers`: If `main.nf` declares containers, `meta.yml`
-  must also contain a non-empty `containers:` block. Run
-  `nf-core modules lint --fix` to auto-correct.
-- `correct_meta_containers`: The containers listed in `meta.yml` must
-  exactly match those parsed from `main.nf`. Run
-  `nf-core modules lint --fix` to auto-correct.
+## meta\_yml\_exists
+
+The `meta.yml` file must exist.
+
+## meta\_yml\_valid
+
+The `meta.yml` must be valid according to the JSON
+schema defined in `modules/meta-schema.json` in the nf-core/modules
+repository.
+
+## meta\_name
+
+The `name` field in `meta.yml` must match (case-insensitive)
+the process name declared in `main.nf`.
+
+## meta\_input
+
+If `main.nf` declares inputs, they must be listed under
+the `input:` key in `meta.yml`.
+
+## correct\_meta\_inputs
+
+The inputs listed in `meta.yml` must exactly
+match those parsed from `main.nf`. Run `nf-core modules lint --fix`
+to auto-correct.
+
+## meta\_output
+
+If `main.nf` declares outputs, they must be listed under
+the `output:` key in `meta.yml`.
+
+## correct\_meta\_outputs
+
+The outputs listed in `meta.yml` must exactly
+match those parsed from `main.nf`. Run `nf-core modules lint --fix`
+to auto-correct.
+
+## has\_meta\_topics
+
+If `main.nf` declares topics, `meta.yml` must
+also contain a non-empty `topics:` block. Run
+`nf-core modules lint --fix` to auto-correct.
+
+## correct\_meta\_topics
+
+The topics listed in `meta.yml` must exactly
+match those parsed from `main.nf`. Run `nf-core modules lint --fix`
+to auto-correct.
+
+## has\_meta\_containers
+
+If `main.nf` declares containers, `meta.yml`
+must also contain a non-empty `containers:` block. Run
+`nf-core modules lint --fix` to auto-correct.
+
+## correct\_meta\_containers
+
+The containers listed in `meta.yml` must
+exactly match those parsed from `main.nf`. Run
+`nf-core modules lint --fix` to auto-correct.
 
 If the module has inputs or outputs, they are expected to be formatted as:
 

sites/docs/src/content/api_reference/dev/module_lint_tests/module_changes.md

@@ -15,5 +15,7 @@ Only runs when linting a pipeline, not the modules repository
 
 The following checks are performed:
 
-- `check_local_copy`: Each module file must be identical to the corresponding
-  file in the remote repository at the pinned commit SHA.
+## check\_local\_copy
+
+Each module file must be identical to the corresponding
+file in the remote repository at the pinned commit SHA.

sites/docs/src/content/api_reference/dev/module_lint_tests/module_deprecations.md

@@ -6,5 +6,7 @@ Check that the modules are up to the latest nf-core standard
 
 The following checks are performed:
 
-- `module_deprecations`: Deprecated files (e.g. `functions.nf`) must not
-  be present in the module directory.
+## module\_deprecations
+
+Deprecated files (e.g. `functions.nf`) must not
+be present in the module directory.

sites/docs/src/content/api_reference/dev/module_lint_tests/module_tests.md

@@ -9,17 +9,43 @@ validates snapshot content, and verifies that nf-test tags follow guidelines.
 
 The following checks are performed:
 
-- `test_dir_exists`: The nf-test directory `tests/` must exist.
-- `test_main_nf_exists`: The file `tests/main.nf.test` must exist.
-- `test_snapshot_exists`: If `snapshot()` is called in `main.nf.test`,
-  the snapshot file `tests/main.nf.test.snap` must exist and be valid JSON.
-- `test_snap_md5sum`: The snapshot must not contain md5sums for empty files
-  (`d41d8cd98f00b204e9800998ecf8427e`) or empty compressed files
-  (`7029066c27ac6f5ef18d660d5741979a`), unless the test name contains `stub`.
-- `test_snap_versions`: The snapshot must contain a `versions` key.
-- `test_main_tags`: The `main.nf.test` file must declare the required tags:
-  `modules`, `modules_<org>`, the full component name, and (for `tool/subtool`
-  modules) the tool name alone. Tags for any chained components included via
-  `include` statements must also be present.
-- `test_old_test_dir`: The legacy pytest directory
-  `tests/modules/<component_name>/` must not exist.
+## test\_dir\_exists
+
+The nf-test directory `tests/` must exist.
+
+## test\_main\_nf\_exists
+
+The file `tests/main.nf.test` must exist.
+
+## test\_snapshot\_exists
+
+If `snapshot()` is called in `main.nf.test`,
+the snapshot file `tests/main.nf.test.snap` must exist and be valid JSON.
+
+## test\_snap\_md5sum
+
+The snapshot must not contain md5sums for empty files
+(`d41d8cd98f00b204e9800998ecf8427e`) or empty compressed files
+(`7029066c27ac6f5ef18d660d5741979a`), unless the test name contains `stub`.
+
+## test\_snap\_versions
+
+The snapshot must contain a `versions` key.
+
+## test\_main\_tags
+
+The `main.nf.test` file must declare the required tags:
+`modules`, `modules_<org>`, the full component name, and (for `tool/subtool`
+modules) the tool name alone. Tags for any chained components included via
+`include` statements must also be present.
+
+## test\_old\_test\_dir
+
+The legacy pytest directory
+`tests/modules/<component_name>/` must not exist.
+
+## test\_stub\_gzip\_syntax
+
+Stub blocks with gzip output files must use the proper syntax. Stub files
+ending in `.gz` must use `echo "" | gzip > file.gz`. Simply touching or
+creating empty `.gz` files will break nf-test’s gzip parser.

sites/docs/src/content/api_reference/dev/module_lint_tests/module_todos.md

@@ -21,8 +21,10 @@ They typically have the following format:
 This lint test runs through all files in the module and searches for these lines.
 If any are found they will throw a warning.
 
-- `module_todo`: A warning is issued for each TODO comment found in the
-  module files.
+## module\_todo
+
+A warning is issued for each TODO comment found in the
+module files.
 
 :::note
 Note that many GUI code editors have plugins to list all instances of _TODO_

sites/docs/src/content/api_reference/dev/module_lint_tests/module_version.md

@@ -10,6 +10,11 @@ newer version of the module available.
 
 The following checks are performed:
 
-- `git_sha`: The module must have a `git_sha` entry in `modules.json`.
-- `module_version`: The module version must match the latest commit in the
-  remote repository. A warning is issued if a newer version is available.
+## git\_sha
+
+The module must have a `git_sha` entry in `modules.json`.
+
+## module\_version
+
+The module version must match the latest commit in the
+remote repository. A warning is issued if a newer version is available.

sites/docs/src/content/api_reference/dev/subworkflow_lint_tests/main_nf.md

@@ -17,8 +17,16 @@ The test checks for the following:
 
 The following checks are performed:
 
-- `main_nf_exists`: The `main.nf` file must exist.
-- `main_nf_script_outputs`: The workflow must have an `emit:` block.
-- `main_nf_version_emitted`: The subworkflow should emit a software version
-  channel. A warning is issued if no `versions` output is found (can be
-  ignored if the subworkflow uses topic channels).
+## main\_nf\_exists
+
+The `main.nf` file must exist.
+
+## main\_nf\_script\_outputs
+
+The workflow must have an `emit:` block.
+
+## main\_nf\_version\_emitted
+
+The subworkflow should emit a software version
+channel. A warning is issued if no `versions` output is found (can be
+ignored if the subworkflow uses topic channels).