nf-core · drpatelh · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021 · Mar 15, 2021
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -354,53 +354,65 @@ def modules(ctx, repository, branch):
 
 @modules.command(help_priority=1)
 @click.pass_context
-def list(ctx):
+@click.argument("pipeline_dir", type=click.Path(exists=True), required=False, metavar="(<pipeline directory>)")
+@click.option("-j", "--json", is_flag=True, help="Print as JSON to stdout")
+def list(ctx, pipeline_dir, json):
     """
     List available software modules.
 
-    Lists all currently available software wrappers in the nf-core/modules repository.
+    If a pipeline directory is given, lists all modules installed locally.
+
+    If no pipeline directory is given, lists all currently available
+    software wrappers in the nf-core/modules repository.
     """
     mods = nf_core.modules.PipelineModules()
     mods.modules_repo = ctx.obj["modules_repo_obj"]
-    print(mods.list_modules())
+    print(mods.list_modules(pipeline_dir, json))
 
 
 @modules.command(help_priority=2)
 @click.pass_context
 @click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
-@click.argument("tool", type=str, required=True, metavar="<tool name>")
+@click.argument("tool", type=str, required=False, metavar="(<tool name>)")
 def install(ctx, pipeline_dir, tool):
     """
     Add a DSL2 software wrapper module to a pipeline.
 
     Given a software name, finds the relevant files in nf-core/modules
     and copies to the pipeline along with associated metadata.
-    """
-    mods = nf_core.modules.PipelineModules()
-    mods.modules_repo = ctx.obj["modules_repo_obj"]
-    mods.pipeline_dir = pipeline_dir
-    mods.install(tool)
-
 
-@modules.command(help_priority=3)
-@click.pass_context
-@click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
-@click.argument("tool", type=str, metavar="<tool name>")
-@click.option("-f", "--force", is_flag=True, default=False, help="Force overwrite of files")
-def update(ctx, tool, pipeline_dir, force):
+    If <tool name> is not supplied on the command line, an interactive fuzzy-finder
+    tool is given with available nf-core module names.
     """
-    Update one or all software wrapper modules.
+    try:
+        mods = nf_core.modules.PipelineModules()
+        mods.modules_repo = ctx.obj["modules_repo_obj"]
+        mods.pipeline_dir = pipeline_dir
+        mods.install(tool)
+    except UserWarning as e:
+        log.critical(e)
+        sys.exit(1)
 
-    Compares a currently installed module against what is available in nf-core/modules.
-    Fetchs files and updates all relevant files for that software wrapper.
 
-    If no module name is specified, loops through all currently installed modules.
-    If no version is specified, looks for the latest available version on nf-core/modules.
-    """
-    mods = nf_core.modules.PipelineModules()
-    mods.modules_repo = ctx.obj["modules_repo_obj"]
-    mods.pipeline_dir = pipeline_dir
-    mods.update(tool, force=force)
+# TODO: Not yet implemented
+# @modules.command(help_priority=3)
+# @click.pass_context
+# @click.argument("pipeline_dir", type=click.Path(exists=True), required=True, metavar="<pipeline directory>")
+# @click.argument("tool", type=str, metavar="<tool name>")
+# def update(ctx, tool, pipeline_dir):
+#     """
+#     Update one or all software wrapper modules.
+#
+#     Compares a currently installed module against what is available in nf-core/modules.
+#     Fetchs files and updates all relevant files for that software wrapper.
+#
+#     If no module name is specified, loops through all currently installed modules.
+#     If no version is specified, looks for the latest available version on nf-core/modules.
+#     """
+#     mods = nf_core.modules.PipelineModules()
+#     mods.modules_repo = ctx.obj["modules_repo_obj"]
+#     mods.pipeline_dir = pipeline_dir
+#     mods.update(tool)
 
 
 @modules.command(help_priority=4)
@@ -411,56 +423,24 @@ def remove(ctx, pipeline_dir, tool):
     """
     Remove a software wrapper from a pipeline.
     """
-    mods = nf_core.modules.PipelineModules()
-    mods.modules_repo = ctx.obj["modules_repo_obj"]
-    mods.pipeline_dir = pipeline_dir
-    mods.remove(tool)
-
-
-@modules.command(help_priority=5)
-@click.pass_context
-def check(ctx):
-    """
-    Check that imported module code has not been modified.
-
-    Compares a software module against the copy on nf-core/modules.
-    If any local modifications are found, the command logs an error
-    and exits with a non-zero exit code.
-
-    Use by the lint tests and automated CI to check that centralised
-    software wrapper code is only modified in the central repository.
-    """
-    mods = nf_core.modules.PipelineModules()
-    mods.modules_repo = ctx.obj["modules_repo_obj"]
-    mods.check_modules()
+    try:
+        mods = nf_core.modules.PipelineModules()
+        mods.modules_repo = ctx.obj["modules_repo_obj"]
+        mods.pipeline_dir = pipeline_dir
+        mods.remove(tool)
+    except UserWarning as e:
+        log.critical(e)
+        sys.exit(1)
 
 
-@modules.command("create", help_priority=6)
+@modules.command("create", help_priority=5)
 @click.pass_context
 @click.argument("directory", type=click.Path(exists=True), required=True, metavar="<directory>")
 @click.argument("tool", type=str, required=True, metavar="<tool/subtool>")
-@click.option("-a", "--author", type=str, metavar="<author>", help="GitHub username")
-@click.option(
-    "-l",
-    "--label",
-    type=str,
-    metavar="<process label>",
-    help="Standard resource label for process i.e. 'process_low', 'process_medium' or 'process_high'",
-)
-@click.option(
-    "-m",
-    "--meta",
-    is_flag=True,
-    default=False,
-    help="Sample information will be provided to module via a 'meta' Groovy map",
-)
-@click.option(
-    "-n",
-    "--no-meta",
-    is_flag=True,
-    default=False,
-    help="Sample information will not be provided to module via a 'meta' Groovy map",
-)
+@click.option("-a", "--author", type=str, metavar="<author>", help="Module author's GitHub username")
+@click.option("-l", "--label", type=str, metavar="<process label>", help="Standard resource label for process")
+@click.option("-m", "--meta", is_flag=True, default=False, help="Use Groovy meta map for sample information")
+@click.option("-n", "--no-meta", is_flag=True, default=False, help="Don't use meta map for sample information")
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
 def create_module(ctx, directory, tool, author, label, meta, no_meta, force):
     """
@@ -470,25 +450,11 @@ def create_module(ctx, directory, tool, author, label, meta, no_meta, force):
     Tool should be named just <tool> or <tool/subtool>
     e.g fastqc or samtools/sort, respectively.
 
-    If <directory> is a pipeline, this function creates a file called:
-    '<directory>/modules/local/tool.nf'
-    OR
-    '<directory>/modules/local/tool_subtool.nf'
-
-    If <directory> is a clone of nf-core/modules, it creates or modifies the following files:
+    If <directory> is a pipeline, this function creates a file called
+    'modules/local/tool_subtool.nf'
 
-    \b
-    modules/software/tool/subtool/
-        * main.nf
-        * meta.yml
-        * functions.nf
-    modules/tests/software/tool/subtool/
-        * main.nf
-        * test.yml
-    tests/config/pytest_software.yml
-
-    The function will attempt to automatically find a Bioconda package called <tool>
-    and matching Docker / Singularity images from BioContainers.
+    If <directory> is a clone of nf-core/modules, it creates or modifies files
+    in 'modules/software', 'modules/tests' and 'tests/config/pytest_software.yml'
     """
     # Combine two bool flags into one variable
     has_meta = None
@@ -508,7 +474,7 @@ def create_module(ctx, directory, tool, author, label, meta, no_meta, force):
         sys.exit(1)
 
 
-@modules.command("create-test-yml", help_priority=7)
+@modules.command("create-test-yml", help_priority=6)
 @click.pass_context
 @click.argument("module", type=str, required=True, metavar="<module name>")
 @click.option("-r", "--run-tests", is_flag=True, default=False, help="Run the test workflows")
@@ -534,7 +500,7 @@ def create_test_yml(ctx, module, run_tests, output, force, no_prompts):
 
 
 ## nf-core schema subcommands
-@nf_core_cli.group(cls=CustomHelpOrder, help_priority=8)
+@nf_core_cli.group(cls=CustomHelpOrder, help_priority=7)
 def schema():
     """
     Suite of tools for developers to manage pipeline schema.

diff --git a/nf_core/launch.py b/nf_core/launch.py
@@ -10,36 +10,15 @@
 import json
 import logging
 import os
-import prompt_toolkit
 import questionary
 import re
 import subprocess
-import textwrap
 import webbrowser
 
 import nf_core.schema, nf_core.utils
 
 log = logging.getLogger(__name__)
 
-# Custom style for questionary
-nfcore_question_style = prompt_toolkit.styles.Style(
-    [
-        ("qmark", "fg:ansiblue bold"),  # token in front of the question
-        ("question", "bold"),  # question text
-        ("answer", "fg:ansigreen nobold"),  # submitted answer text behind the question
-        ("pointer", "fg:ansiyellow bold"),  # pointer used in select and checkbox prompts
-        ("highlighted", "fg:ansiblue bold"),  # pointed-at choice in select and checkbox prompts
-        ("selected", "fg:ansigreen noreverse"),  # style for a selected item of a checkbox
-        ("separator", "fg:ansiblack"),  # separator in lists
-        ("instruction", ""),  # user instructions for select, rawselect, checkbox
-        ("text", ""),  # plain text
-        ("disabled", "fg:gray italic"),  # disabled choices for select and checkbox prompts
-        ("choice-default", "fg:ansiblack"),
-        ("choice-default-changed", "fg:ansiyellow"),
-        ("choice-required", "fg:ansired"),
-    ]
-)
-
 
 class Launch(object):
     """ Class to hold config option to launch a pipeline """
@@ -268,7 +247,7 @@ def prompt_web_gui(self):
             "choices": ["Web based", "Command line"],
             "default": "Web based",
         }
-        answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+        answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
         return answer["use_web_gui"] == "Web based"
 
     def launch_web_gui(self):
@@ -405,12 +384,12 @@ def prompt_param(self, param_id, param_obj, is_required, answers):
 
         # Print the question
         question = self.single_param_to_questionary(param_id, param_obj, answers)
-        answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+        answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
         # If required and got an empty reponse, ask again
         while type(answer[param_id]) is str and answer[param_id].strip() == "" and is_required:
             log.error("'–-{}' is required".format(param_id))
-            answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
 
         # Ignore if empty
         if answer[param_id] == "":
@@ -480,7 +459,7 @@ def prompt_group(self, group_id, group_obj):
             if len(question["choices"]) == 2:
                 return {}
 
-            answer = questionary.unsafe_prompt([question], style=nfcore_question_style)
+            answer = questionary.unsafe_prompt([question], style=nf_core.utils.nfcore_question_style)
             if answer[group_id] == "Continue >>":
                 while_break = True
                 # Check if there are any required parameters that don't have answers

diff --git a/nf_core/list.py b/nf_core/list.py
@@ -258,7 +258,6 @@ def sort_pulled_date(wf):
                 table.add_row(*rowdata, style="dim")
             else:
                 table.add_row(*rowdata)
-        t_headers = ["Name", "Latest Release", "Released", "Last Pulled", "Have latest release?"]
 
         # Print summary table
         return table

diff --git a/nf_core/module-template/cookiecutter.json b/nf_core/module-template/cookiecutter.json
diff --git a/...ecutter.tool_name}}/software/functions.nf → ...ore/module-template/software/functions.nf b/...ecutter.tool_name}}/software/functions.nf → ...ore/module-template/software/functions.nf
diff --git a/...cookiecutter.tool_name}}/software/main.nf → nf_core/module-template/software/main.nf b/...cookiecutter.tool_name}}/software/main.nf → nf_core/module-template/software/main.nf
@@ -20,22 +20,22 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 options        = initOptions(params.options)
 
-process {{ cookiecutter.tool_name_upper }} {
-    {{ 'tag "$meta.id"' if cookiecutter.has_meta else "'$bam'" }}
-    label '{{ cookiecutter.label }}'
+process {{ tool_name|upper }} {
+    {{ 'tag "$meta.id"' if has_meta else "'$bam'" }}
+    label '{{ label }}'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:{{ 'meta.id' if cookiecutter.has_meta else "''" }}) }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:{{ 'meta.id' if has_meta else "''" }}) }
 
     // TODO nf-core: List required Conda package(s).
     //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda (params.enable_conda ? "{{ cookiecutter.bioconda if cookiecutter.bioconda else 'YOUR-TOOL-HERE' }}" : null)
+    conda (params.enable_conda ? "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/{{ cookiecutter.container_tag if cookiecutter.container_tag else 'YOUR-TOOL-HERE' }}"
+        container "https://depot.galaxyproject.org/singularity/{{ container_tag if container_tag else 'YOUR-TOOL-HERE' }}"
     } else {
-        container "quay.io/biocontainers/{{ cookiecutter.container_tag if cookiecutter.container_tag else 'YOUR-TOOL-HERE' }}"
+        container "quay.io/biocontainers/{{ container_tag if container_tag else 'YOUR-TOOL-HERE' }}"
     }
 
     input:
@@ -45,19 +45,19 @@ process {{ cookiecutter.tool_name_upper }} {
     //               https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
     // TODO nf-core: Where applicable please provide/convert compressed files as input/output
     //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    {{ 'tuple val(meta), path(bam)' if cookiecutter.has_meta else 'path bam' }}
+    {{ 'tuple val(meta), path(bam)' if has_meta else 'path bam' }}
 
     output:
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    {{ 'tuple val(meta), path("*.bam")' if cookiecutter.has_meta else 'path "*.bam"' }}   , emit: bam
+    {{ 'tuple val(meta), path("*.bam")' if has_meta else 'path "*.bam"' }}, emit: bam
     // TODO nf-core: List additional required output channels/values here
     path "*.version.txt"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
-    {% if cookiecutter.has_meta %}
+    {% if has_meta -%}
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    {% endif %}
+    {%- endif %}
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
     //               e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
@@ -71,8 +71,10 @@ process {{ cookiecutter.tool_name_upper }} {
         sort \\
         $options.args \\
         -@ $task.cpus \\
+        {%- if has_meta %}
         -o ${prefix}.bam \\
         -T $prefix \\
+        {%- endif %}
         $bam
 
     echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt