nf-core · mirpedrol · Oct 6, 2022 · Sep 23, 2022 · Sep 23, 2022 · Sep 23, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@
 
 ### Template
 
+- Add template for subworkflows
 - Add `actions/upload-artifact` step to the awstest workflows, to expose the debug log file
 - Add `prettier` as a requirement to Gitpod Dockerimage
 - Bioconda incompatible conda channel setups now result in more informative error messages ([#1812](https://github.com/nf-core/tools/pull/1812))
@@ -41,6 +42,7 @@
 - Schema: Remove `allOf` if no definition groups are left.
 - Use contextlib to temporarily change working directories ([#1819](https://github.com/nf-core/tools/pull/1819))
 - More helpful error messages if `nf-core download` can't parse a singularity image download
+- Add `nf-core subworkflows create` command
 
 ### Modules
 

diff --git a/nf_core/__main__.py b/nf_core/__main__.py
@@ -20,6 +20,7 @@
 import nf_core.list
 import nf_core.modules
 import nf_core.schema
+import nf_core.subworkflows
 import nf_core.sync
 import nf_core.utils
 
@@ -54,6 +55,12 @@
             "commands": ["create", "create-test-yml", "lint", "bump-versions", "mulled", "test"],
         },
     ],
+    "nf-core subworkflows": [
+        {
+            "name": "Developing new subworkflows",
+            "commands": ["create"],
+        },
+    ],
 }
 click.rich_click.OPTION_GROUPS = {
     "nf-core modules list local": [{"options": ["--dir", "--json", "--help"]}],
@@ -89,7 +96,7 @@ def run_nf_core():
         log.debug(f"Could not check latest version: {e}")
     stderr.print("\n")
 
-    # Lanch the click cli
+    # Launch the click cli
     nf_core_cli(auto_envvar_prefix="NFCORE")
 
 
@@ -383,6 +390,38 @@ def modules(ctx, git_remote, branch, no_pull):
     ctx.obj["modules_repo_no_pull"] = no_pull
 
 
+# nf-core subworkflows click command
+@nf_core_cli.group()
+@click.option(
+    "-g",
+    "--git-remote",
+    type=str,
+    default=nf_core.modules.modules_repo.NF_CORE_MODULES_REMOTE,
+    help="Remote git repo to fetch files from",
+)
+@click.option("-b", "--branch", type=str, default=None, help="Branch of git repository hosting modules.")
+@click.option(
+    "-N",
+    "--no-pull",
+    is_flag=True,
+    default=False,
+    help="Do not pull in latest changes to local clone of modules repository.",
+)
+@click.pass_context
+def subworkflows(ctx, git_remote, branch, no_pull):
+    """
+    Commands to manage Nextflow DSL2 subworkflows (tool wrappers).
+    """
+    # ensure that ctx.obj exists and is a dict (in case `cli()` is called
+    # by means other than the `if` block below)
+    ctx.ensure_object(dict)
+
+    # Place the arguments in a context object
+    ctx.obj["subworkflows_repo_url"] = git_remote
+    ctx.obj["subworkflows_repo_branch"] = branch
+    ctx.obj["subworkflows_repo_no_pull"] = no_pull
+
+
 # nf-core modules list subcommands
 @modules.group()
 @click.pass_context
@@ -855,6 +894,36 @@ def test_module(ctx, tool, no_prompts, pytest_args):
         sys.exit(1)
 
 
+# nf-core subworkflows create
+@subworkflows.command("create")
+@click.pass_context
+@click.argument("subworkflow", type=str, required=False, metavar="subworkflow name")
+@click.option("-d", "--dir", type=click.Path(exists=True), default=".", metavar="<directory>")
+@click.option("-a", "--author", type=str, metavar="<author>", help="Module author's GitHub username prefixed with '@'")
+@click.option("-f", "--force", is_flag=True, default=False, help="Overwrite any files if they already exist")
+def create_subworkflow(ctx, subworkflow, dir, author, force):
+    """
+    Create a new subworkflow from the nf-core template.
+
+    If the specified directory is a pipeline, this function creates a file called
+    'subworkflows/local/<subworkflow_name>.nf'
+
+    If the specified directory is a clone of nf-core/modules, it creates or modifies files
+    in 'subworkflows/', 'tests/subworkflows' and 'tests/config/pytest_modules.yml'
+    """
+
+    # Run function
+    try:
+        subworkflow_create = nf_core.subworkflows.SubworkflowCreate(dir, subworkflow, author, force)
+        subworkflow_create.create()
+    except UserWarning as e:
+        log.critical(e)
+        sys.exit(1)
+    except LookupError as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core schema subcommands
 @nf_core_cli.group()
 def schema():

diff --git a/nf_core/modules/create.py b/nf_core/modules/create.py
@@ -142,7 +142,7 @@ def create(self):
 
         self.tool_name_underscore = self.tool_name.replace("/", "_")
 
-        # Check existance of directories early for fast-fail
+        # Check existence of directories early for fast-fail
         self.file_paths = self.get_module_dirs()
 
         # Try to find a bioconda package for 'tool'
@@ -246,7 +246,7 @@ def create(self):
                 "[violet]Will the module require a meta map of sample information?", default=True
             )
 
-        # Create module template with cokiecutter
+        # Create module template with jinja
         self.render_template()
 
         if self.repo_type == "modules":

diff --git a/nf_core/subworkflow-template/subworkflows/main.nf b/nf_core/subworkflow-template/subworkflows/main.nf
@@ -0,0 +1,37 @@
+// TODO nf-core: If in doubt look at other nf-core/subworkflows to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/subworkflows
+//               You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A subworkflow SHOULD only import modules not other subworkflows
+// TODO nf-core: A subworkflow SHOULD import at least two modules
+
+include { SAMTOOLS_SORT      } from '../../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX     } from '../../../modules/nf-core/samtools/index/main'
+
+workflow {{ subworkflow_name|upper }} {
+
+    take:
+    // TODO nf-core: edit input (take) channels
+    ch_bam // channel: [ val(meta), [ bam ] ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    // TODO nf-core: substitute modules here for the modules of your subworkflow
+
+    SAMTOOLS_SORT ( ch_bam )
+    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
+
+    SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam )
+    ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
+
+    emit:
+    // TODO nf-core: edit emitted channels
+    bam      = SAMTOOLS_SORT.out.bam           // channel: [ val(meta), [ bam ] ]
+    bai      = SAMTOOLS_INDEX.out.bai          // channel: [ val(meta), [ bai ] ]
+    csi      = SAMTOOLS_INDEX.out.csi          // channel: [ val(meta), [ csi ] ]
+
+    versions = ch_versions                     // channel: [ versions.yml ]
+}
+
diff --git a/nf_core/subworkflow-template/subworkflows/meta.yml b/nf_core/subworkflow-template/subworkflows/meta.yml
@@ -0,0 +1,48 @@
+name: "{{ subworkflow_name }}"
+## TODO nf-core: Add a description of the subworkflow and list keywords
+description: Sort SAM/BAM/CRAM file
+keywords:
+  - sort
+  - bam
+  - sam
+  - cram
+## TODO nf-core: Add a list of the modules used in the subworkflow
+modules:
+  - samtools/sort
+  - samtools/index
+## TODO nf-core: List all of the variables used as input, including their types and descriptions
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+## TODO nf-core: List all of the variables used as output, including their types and descriptions
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - bai:
+      type: file
+      description: BAM/CRAM/SAM samtools index
+      pattern: "*.{bai,crai,sai}"
+  - csi:
+      type: file
+      description: CSI samtools index
+      pattern: "*.csi"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "{{ author }}"
diff --git a/nf_core/subworkflow-template/tests/main.nf b/nf_core/subworkflow-template/tests/main.nf
@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { {{ subworkflow_name|upper }} } from '../../../../subworkflows/nf-core/{{ subworkflow_dir }}/main.nf'
+
+workflow test_{{ subworkflow_name }} {
+    {% if has_meta %}
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+    {%- else %}
+    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+    {%- endif %}
+
+    {{ subworkflow_name|upper }} ( input )
+}
diff --git a/nf_core/subworkflow-template/tests/nextflow.config b/nf_core/subworkflow-template/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/nf_core/subworkflow-template/tests/test.yml b/nf_core/subworkflow-template/tests/test.yml
@@ -0,0 +1,12 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core subworkflows create-test-yml {{ subworkflow_name_underscore }}
+
+- name: "{{ subworkflow_name }}"
+  command: nextflow run ./tests/subworkflows/nf-core/{{ subworkflow_dir }} -entry test_{{ subworkflow_name }} -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/{{ subworkflow_dir }}/nextflow.config
+  tags:
+    - "{{ subworkflow_name }}"
+  files:
+    - path: "output/{{ subworkflow_name }}/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/{{ subworkflow_name }}/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
diff --git a/nf_core/subworkflows/__init__.py b/nf_core/subworkflows/__init__.py
@@ -0,0 +1 @@
+from .create import SubworkflowCreate