modify template to use nf-validation plugin

.github/CONTRIBUTING.md

@@ -142,4 +142,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/workflows/pytest-frozen-ubuntu-20.04.yml

@@ -15,7 +15,7 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  pytest:
+  pytest-frozen:
     runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v3

CHANGELOG.md

@@ -11,6 +11,15 @@
 - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286)
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
+- Fix link in the MultiQC report to point to exact version of output docs ([#2298](https://github.com/nf-core/tools/pull/2298))
+- Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Generate input channel from input file using Nextflow nf-validation plugin ([#1771](https://github.com/nf-core/tools/pull/1771/))
+
+
+### Download
+
+- Introduce a `--tower` flag for `nf-core download` to obtain pipelines in an offline format suited for [seqeralabs® Nextflow Tower](https://cloud.tower.nf/) ([#2247](https://github.com/nf-core/tools/pull/2247)).
+- Refactored the CLI for `--singularity-cache` in `nf-core download` from a flag to an argument. The prior options were renamed to `amend` (container images are only saved in the `$NXF_SINGULARITY_CACHEDIR`) and `copy` (a copy of the image is saved with the download). `remote` was newly introduced and allows to provide a table of contents of a remote cache via an additional argument `--singularity-cache-index` ([#2247](https://github.com/nf-core/tools/pull/2247)).
 
 ### Linting
 

README.md

@@ -20,7 +20,7 @@ A python package with helper tools for the nf-core community.
 - [`nf-core` tools update](#update-tools)
 - [`nf-core list` - List available pipelines](#listing-pipelines)
 - [`nf-core launch` - Run a pipeline with interactive parameter prompts](#launch-a-pipeline)
-- [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use)
+- [`nf-core download` - Download a pipeline for offline use](#downloading-pipelines-for-offline-use)
 - [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences)
 - [`nf-core create` - Create a new pipeline with the nf-core template](#creating-a-new-pipeline)
 - [`nf-core lint` - Check pipeline code against nf-core guidelines](#linting-a-workflow)
@@ -348,13 +348,13 @@ nextflow run /path/to/download/nf-core-rnaseq-dev/workflow/ --input mydata.csv -
 ### Downloaded nf-core configs
 
 The pipeline files are automatically updated (`params.custom_config_base` is set to `../configs`), so that the local copy of institutional configs are available when running the pipeline.
-So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs).
+So using `-profile <NAME>` should work if available within [nf-core/configs](https://github.com/nf-core/configs). This option is not available when downloading a pipeline for use with [Nextflow Tower](#adapting-downloads-to-nextflow-tower) because the application manages all configurations separately.
 
 ### Downloading singularity containers
 
 If you're using Singularity, the `nf-core download` command can also fetch the required Singularity container images for you.
 To do this, select `singularity` in the prompt or specify `--container singularity` in the command.
-Your archive / target output directory will then include three folders: `workflow`, `configs` and also `singularity-containers`.
+Your archive / target output directory will then also include a separate folder `singularity-containers`.
 
 The downloaded workflow files are again edited to add the following line to the end of the pipeline's `nextflow.config` file:
 
@@ -372,10 +372,9 @@ We highly recommend setting the `$NXF_SINGULARITY_CACHEDIR` environment variable
 If found, the tool will fetch the Singularity images to this directory first before copying to the target output archive / directory.
 Any images previously fetched will be found there and copied directly - this includes images that may be shared with other pipelines or previous pipeline version downloads or download attempts.
 
-If you are running the download on the same system where you will be running the pipeline (eg. a shared filesystem where Nextflow won't have an internet connection at a later date), you can choose to _only_ use the cache via a prompt or cli options `--singularity-cache-only` / `--singularity-cache-copy`.
+If you are running the download on the same system where you will be running the pipeline (eg. a shared filesystem where Nextflow won't have an internet connection at a later date), you can choose to _only_ use the cache via a prompt or cli options `--singularity-cache amend`. This instructs `nf-core download` to fetch all Singularity images to the `$NXF_SINGULARITY_CACHEDIR` directory but does _not_ copy them to the workflow archive / directory. The workflow config file is _not_ edited. This means that when you later run the workflow, Nextflow will just use the cache folder directly.
 
-This instructs `nf-core download` to fetch all Singularity images to the `$NXF_SINGULARITY_CACHEDIR` directory but does _not_ copy them to the workflow archive / directory.
-The workflow config file is _not_ edited. This means that when you later run the workflow, Nextflow will just use the cache folder directly.
+If you are downloading a workflow for a different system, you can provide information about its image cache to `nf-core download`. To avoid unnecessary container image downloads, choose `--singularity-cache remote` and provide a list of already available images as plain text file to `--singularity-cache-index my_list_of_remotely_available_images.txt`. To generate this list on the remote system, run `find $NXF_SINGULARITY_CACHEDIR -name "*.img" > my_list_of_remotely_available_images.txt`. The tool will then only download and copy images into your output directory, which are missing on the remote system.
 
 #### How the Singularity image downloads work
 
@@ -391,16 +390,22 @@ Where both are found, the download URL is preferred.
 
 Once a full list of containers is found, they are processed in the following order:
 
-1. If the target image already exists, nothing is done (eg. with `$NXF_SINGULARITY_CACHEDIR` and `--singularity-cache-only` specified)
-2. If found in `$NXF_SINGULARITY_CACHEDIR` and `--singularity-cache-only` is _not_ specified, they are copied to the output directory
+1. If the target image already exists, nothing is done (eg. with `$NXF_SINGULARITY_CACHEDIR` and `--singularity-cache amend` specified)
+2. If found in `$NXF_SINGULARITY_CACHEDIR` and `--singularity-cache copy` is specified, they are copied to the output directory
 3. If they start with `http` they are downloaded directly within Python (default 4 at a time, you can customise this with `--parallel-downloads`)
 4. If they look like a Docker image name, they are fetched using a `singularity pull` command
-   - This requires Singularity to be installed on the system and is substantially slower
+   - This requires Singularity/Apptainer to be installed on the system and is substantially slower
 
-Note that compressing many GBs of binary files can be slow, so specifying `--compress none` is recommended when downloading Singularity images.
+Note that compressing many GBs of binary files can be slow, so specifying `--compress none` is recommended when downloading Singularity images that are copied to the output directory.
 
 If the download speeds are much slower than your internet connection is capable of, you can set `--parallel-downloads` to a large number to download loads of images at once.
 
+### Adapting downloads to Nextflow Tower
+
+[seqeralabs® Nextflow Tower](https://cloud.tower.nf/) provides a graphical user interface to oversee pipeline runs, gather statistics and configure compute resources. While pipelines added to _Tower_ are preferably hosted at a Git service, providing them as disconnected, self-reliant repositories is also possible for premises with restricted network access. Choosing the `--tower` flag will download the pipeline in an appropriate form.
+
+Subsequently, the `*.git` folder can be moved to it's final destination and linked with a pipeline in _Tower_ using the `file:/` prefix.
+
 ## Pipeline software licences
 
 Sometimes it's useful to see the software licences of the tools used in a pipeline.

nf_core/__main__.py

@@ -209,21 +209,46 @@ def launch(pipeline, id, revision, command_only, params_in, params_out, save_all
 # nf-core download
 @nf_core_cli.command()
 @click.argument("pipeline", required=False, metavar="<pipeline name>")
-@click.option("-r", "--revision", type=str, help="Pipeline release")
+@click.option(
+    "-r",
+    "--revision",
+    multiple=True,
+    help="Pipeline release to download. Multiple invocations are possible, e.g. `-r 1.1 -r 1.2`",
+)
 @click.option("-o", "--outdir", type=str, help="Output directory")
 @click.option(
     "-x", "--compress", type=click.Choice(["tar.gz", "tar.bz2", "zip", "none"]), help="Archive compression type"
 )
 @click.option("-f", "--force", is_flag=True, default=False, help="Overwrite existing files")
+@click.option("-t", "--tower", is_flag=True, default=False, help="Download for seqeralabs® Nextflow Tower")
 @click.option(
     "-c", "--container", type=click.Choice(["none", "singularity"]), help="Download software container images"
 )
 @click.option(
-    "--singularity-cache-only/--singularity-cache-copy",
-    help="Don't / do copy images to the output directory and set 'singularity.cacheDir' in workflow",
+    "-s",
+    "--singularity-cache",
+    type=click.Choice(["amend", "copy", "remote"]),
+    help="Utilize the 'singularity.cacheDir' in the download process, if applicable.",
+)
+@click.option(
+    "-i",
+    "--singularity-cache-index",
+    type=str,
+    help="List of images already available in a remote 'singularity.cacheDir', imposes --singularity-cache=remote",
 )
 @click.option("-p", "--parallel-downloads", type=int, default=4, help="Number of parallel image downloads")
-def download(pipeline, revision, outdir, compress, force, container, singularity_cache_only, parallel_downloads):
+def download(
+    pipeline,
+    revision,
+    outdir,
+    compress,
+    force,
+    tower,
+    container,
+    singularity_cache,
+    singularity_cache_index,
+    parallel_downloads,
+):
     """
     Download a pipeline, nf-core/configs and pipeline singularity images.
 
@@ -233,7 +258,16 @@ def download(pipeline, revision, outdir, compress, force, container, singularity
     from nf_core.download import DownloadWorkflow
 
     dl = DownloadWorkflow(
-        pipeline, revision, outdir, compress, force, container, singularity_cache_only, parallel_downloads
+        pipeline,
+        revision,
+        outdir,
+        compress,
+        force,
+        tower,
+        container,
+        singularity_cache,
+        singularity_cache_index,
+        parallel_downloads,
     )
     dl.download_workflow()
 

nf_core/bump_version.py

@@ -3,8 +3,8 @@
 """
 
 import logging
-import os
 import re
+from pathlib import Path
 
 import rich.console
 
@@ -44,6 +44,17 @@ def bump_pipeline_version(pipeline_obj, new_version):
             )
         ],
     )
+    # multiqc_config.yaml
+    update_file_version(
+        Path("assets", "multiqc_config.yml"),
+        pipeline_obj,
+        [
+            (
+                rf"{re.escape(current_version)}",
+                f"{new_version}",
+            )
+        ],
+    )
 
 
 def bump_nextflow_version(pipeline_obj, new_version):
@@ -77,7 +88,7 @@ def bump_nextflow_version(pipeline_obj, new_version):
 
     # .github/workflows/ci.yml - Nextflow version matrix
     update_file_version(
-        os.path.join(".github", "workflows", "ci.yml"),
+        Path(".github", "workflows", "ci.yml"),
         pipeline_obj,
         [
             (