Data was processed using nf-core/airrflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).
+ Data was processed using nf-core/airrflow v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index e8e62182..889351d6 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
-report_comment: >
- This report has been generated by the
nf-core/airrflow
+report_comment:
+ This report has been generated by the
nf-core/airrflow
analysis pipeline. For information about how to interpret these results, please see the
documentation.
diff --git a/assets/nf-core-airrflow_logo_light.png b/assets/nf-core-airrflow_logo_light.png
index bf5a8518..2c7265f7 100644
Binary files a/assets/nf-core-airrflow_logo_light.png and b/assets/nf-core-airrflow_logo_light.png differ
diff --git a/assets/schema_input.json b/assets/schema_input.json
new file mode 100644
index 00000000..327564f0
--- /dev/null
+++ b/assets/schema_input.json
@@ -0,0 +1,65 @@
+{
+ "$schema": "http://json-schema.org/draft-07/schema",
+ "$id": "https://raw.githubusercontent.com/nf-core/airrflow/master/assets/schema_input.json",
+ "title": "nf-core/airrflow pipeline - params.input schema",
+ "description": "Schema for the file provided with params.input",
+ "type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "sample_id": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Sample name must be provided and cannot contain spaces."
+ },
+ "subject_id": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Subject name must be provided and cannot contain spaces."
+ },
+ "species": {
+ "type": "string",
+ "enum": ["mouse", "human"],
+ "errorMessage": "Species name must be provided and must be one of: mouse, human."
+ },
+ "pcr_target_locus": {
+ "type": "string",
+ "enum": ["TR", "IG", "ig", "tr", "Ig", "Tr"],
+ "errorMessage": "PCR target locus must be provided and must be one of: TR, IG."
+ },
+ "tissue": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Tissue name must be provided and cannot contain spaces."
+ },
+ "sex": {
+ "type": "string",
+ "pattern": "^\\S+$",
+ "errorMessage": "Sex must be provided, specify NA if unknown."
+ },
+ "age": {
+ "type": "string",
+ "errorMessage": "Age must be provided, specify NA if unknown."
+ },
+ "biomaterial_provider": {
+ "type": "string",
+ "errorMessage": "Biomaterial provider must be provided."
+ },
+ "single_cell": {
+ "type": "boolean",
+ "pattern": "^\\S+$",
+ "errorMessage": "Single cell must be provided as a TRUE/FALSE value."
+ }
+ },
+ "required": [
+ "sample_id",
+ "subject_id",
+ "species",
+ "pcr_target_locus",
+ "tissue",
+ "sex",
+ "age",
+ "biomaterial_provider"
+ ]
+ }
+}
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 043d02f2..bd9523d9 100644
--- a/assets/slackreport.json
+++ b/assets/slackreport.json
@@ -3,7 +3,7 @@
{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
- "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+ "author_name": "nf-core/airrflow v${version} - ${runName}",
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
"fields": [
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index 355caec3..39c2514e 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -86,7 +86,6 @@ def check_samplesheet(file_in, assembled):
"subject_id",
"species",
"pcr_target_locus",
- "tissue",
]
no_whitespaces_assembled = [
"sample_id",
diff --git a/conf/modules.config b/conf/modules.config
index 029b68af..65b31c5a 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -178,12 +178,15 @@ process {
]
}
- withName: PRESTO_BUILDCONSENSUS {
+ withName: PRESTO_BUILDCONSENSUS_UMI {
publishDir = [
path: { "${params.outdir}/presto/06-build-consensus/${meta.id}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
+ ext.args = ''
+ ext.args2 = ''
+ ext.args3 = 'ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT'
}
withName: PRESTO_POSTCONSENSUS_PAIRSEQ {
@@ -434,6 +437,12 @@ process {
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
+ ext.args = ['findthreshold_method':'gmm',
+ 'findthreshold_model':'gamma-norm',
+ 'findthreshold_edge':0.9,
+ 'findthreshold_cutoff':'user',
+ 'findthreshold_spc':0.995,
+ 'subsample':10000]
}
withName: DEFINE_CLONES_COMPUTE {
@@ -445,7 +454,7 @@ process {
ext.args = ['outname':'', 'model':'hierarchical',
'method':'nt', 'linkage':'single',
'skip_convergence':true,
- 'outputby':'sample_id', 'min_n':30]
+ 'min_n':30]
}
withName: DEFINE_CLONES_REPORT {
@@ -457,7 +466,7 @@ process {
ext.args = ['outname':'', 'model':'hierarchical',
'method':'nt', 'linkage':'single',
'skip_convergence':false,
- 'outputby':'sample_id', 'min_n':30]
+ 'min_n':30]
}
withName: DOWSER_LINEAGES {
diff --git a/conf/test_full.config b/conf/test_full.config
index 52781925..8196a9d3 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -28,3 +28,12 @@ params {
umi_start = 0
umi_position = 'R1'
}
+
+process {
+ withName:DOWSER_LINEAGES{
+ ext.args = ['build':'igphyml',
+ 'minseq':5,
+ 'traits':'c_primer',
+ 'tips':'c_primer']
+ }
+}
diff --git a/docs/output.md b/docs/output.md
index e2477c8d..cf269b42 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -388,10 +388,10 @@ This folder is genereated when `detect_contamination` is set to `true`.
- `clonal_analysis/find_threshold/`
- `*log`: Log of the process that will be parsed to generate a report.
- - `all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
- Junction regions as determined by Shazam.
- - `all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.
- `all_reps_dist_report`: Report
+ - `tables/all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
+ Junction regions as determined by Shazam.
+ - `tables/all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.
diff --git a/docs/usage.md b/docs/usage.md
index 712fbe3f..356b82bd 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -4,15 +4,15 @@
> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._
-# Introduction
+## Introduction
The nf-core/airrflow pipeline allows processing BCR and TCR targeted sequencing data from bulk and single-cell sequencing protocols. It performs sequence assembly, V(D)J assignment, clonotyping, lineage reconsctruction and repertoire analysis using the [Immcantation](https://immcantation.readthedocs.io/en/stable/) framework.
-# Running the pipeline
+## Running the pipeline
-## Quickstart
+### Quickstart
A typical command for running the pipeline for **bulk raw fastq files** is:
@@ -39,6 +39,7 @@ nextflow run nf-core/airrflow \
--outdir results
```
+Check the section [Input samplesheet](#input-samplesheet) below for instructions on how to create the samplesheet, and the [Supported library generation protocols](#supported-bulk-library-generation-methods-protocols) section below for examples on how to run the pipeline for different bulk sequencing protocols.
For more information about the parameters, please refer to the [parameters documentation](https://nf-co.re/airrflow/parameters).
The command above will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -56,7 +57,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
Pipeline settings can be provided in a `yaml` or `json` file via `-params-file
`.
> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
-> The above pipeline run specified with a params file in yaml format:
+
+The above pipeline run specified with a params file in yaml format:
```bash
nextflow run nf-core/airrflow -profile docker -params-file params.yaml
@@ -68,12 +70,31 @@ with `params.yaml` containing:
input: './samplesheet.csv'
outdir: './results/'
genome: 'GRCh37'
-input: 'data'
<...>
```
You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
+## Updating the pipeline
+
+When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
+
+```bash
+nextflow pull nf-core/airrflow
+```
+
+## Reproducibility
+
+It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
+
+First, go to the [nf-core/airrflow releases page](https://github.com/nf-core/airrflow/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
+
+This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
+
+To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+
+> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+
## Input samplesheet
### Fastq input samplesheet (bulk sequencing only)
@@ -344,27 +365,7 @@ The UMI barcodes are typically read from an index file but sometimes can be prov
- No UMIs in R1 or R2 reads: if no UMIs are present in the samples, specify `--umi_length 0` to use the sans-UMI subworkflow.
-## Updating the pipeline
-
-When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:
-
-```bash
-nextflow pull nf-core/airrflow
-```
-
-## Reproducibility
-
-It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
-
-First, go to the [nf-core/airrflow releases page](https://github.com/nf-core/airrflow/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
-
-This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports.
-
-To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
-
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
-
-# Core Nextflow arguments
+## Core Nextflow arguments
> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
@@ -401,58 +402,58 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- `conda`
- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
-## `-resume`
+### `-resume`
Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html).
You can also supply a run name to resume a specific run: `-resume [run-name]`. Use the `nextflow log` command to show previous run names.
-## `-c`
+### `-c`
Specify the path to a specific config file (this is a core Nextflow command). See the [nf-core website documentation](https://nf-co.re/usage/configuration) for more information.
-## Nextflow memory requirements
-
-In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
-We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
-
-```bash
-NXF_OPTS='-Xms1g -Xmx4g'
-```
-
-## Running in the background
-
-Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
-
-The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.
-
-Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
-Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
-
-# Custom configuration
+## Custom configuration
-## Resource requests
+### Resource requests
Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped.
To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website.
-## Custom Containers
+### Custom Containers
In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version may be out of date.
To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website.
-## Custom Tool Arguments
+### Custom Tool Arguments
A pipeline might not always support every possible argument or option of a particular tool used in pipeline. Fortunately, nf-core pipelines provide some freedom to users to insert additional parameters that the pipeline does not include by default.
To learn how to provide additional arguments to a particular tool of the pipeline, please see the [customising tool arguments](https://nf-co.re/docs/usage/configuration#customising-tool-arguments) section of the nf-core website.
-## nf-core/configs
+### nf-core/configs
In most cases, you will only need to create a custom config as a one-off but if you and others within your organisation are likely to be running nf-core pipelines regularly and need to use the same settings regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter. You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile.
See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information about creating your own configuration files.
If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack) on the [`#configs` channel](https://nfcore.slack.com/channels/configs).
+
+## Running in the background
+
+Nextflow handles job submissions and supervises the running jobs. The Nextflow process must run until the pipeline is finished.
+
+The Nextflow `-bg` flag launches Nextflow in the background, detached from your terminal so that the workflow does not stop if you log out of your session. The logs are saved to a file.
+
+Alternatively, you can use `screen` / `tmux` or similar tool to create a detached session which you can log back into at a later time.
+Some HPC setups also allow you to run nextflow within a cluster job submitted your job scheduler (from where it submits more jobs).
+
+## Nextflow memory requirements
+
+In some cases, the Nextflow Java virtual machines can start to request a large amount of memory.
+We recommend adding the following line to your environment to limit this (typically in `~/.bashrc` or `~./bash_profile`):
+
+```bash
+NXF_OPTS='-Xms1g -Xmx4g'
+```
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
deleted file mode 100755
index 9b34804d..00000000
--- a/lib/NfcoreSchema.groovy
+++ /dev/null
@@ -1,530 +0,0 @@
-//
-// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
-//
-
-import nextflow.Nextflow
-import org.everit.json.schema.Schema
-import org.everit.json.schema.loader.SchemaLoader
-import org.everit.json.schema.ValidationException
-import org.json.JSONObject
-import org.json.JSONTokener
-import org.json.JSONArray
-import groovy.json.JsonSlurper
-import groovy.json.JsonBuilder
-
-class NfcoreSchema {
-
- //
- // Resolve Schema path relative to main workflow directory
- //
- public static String getSchemaPath(workflow, schema_filename='nextflow_schema.json') {
- return "${workflow.projectDir}/${schema_filename}"
- }
-
- //
- // Function to loop over all parameters defined in schema and check
- // whether the given parameters adhere to the specifications
- //
- /* groovylint-disable-next-line UnusedPrivateMethodParameter */
- public static void validateParameters(workflow, params, log, schema_filename='nextflow_schema.json') {
- def has_error = false
- //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
- // Check for nextflow core params and unexpected params
- def json = new File(getSchemaPath(workflow, schema_filename=schema_filename)).text
- def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions')
- def nf_params = [
- // Options for base `nextflow` command
- 'bg',
- 'c',
- 'C',
- 'config',
- 'd',
- 'D',
- 'dockerize',
- 'h',
- 'log',
- 'q',
- 'quiet',
- 'syslog',
- 'v',
-
- // Options for `nextflow run` command
- 'ansi',
- 'ansi-log',
- 'bg',
- 'bucket-dir',
- 'c',
- 'cache',
- 'config',
- 'dsl2',
- 'dump-channels',
- 'dump-hashes',
- 'E',
- 'entry',
- 'latest',
- 'lib',
- 'main-script',
- 'N',
- 'name',
- 'offline',
- 'params-file',
- 'pi',
- 'plugins',
- 'poll-interval',
- 'pool-size',
- 'profile',
- 'ps',
- 'qs',
- 'queue-size',
- 'r',
- 'resume',
- 'revision',
- 'stdin',
- 'stub',
- 'stub-run',
- 'test',
- 'w',
- 'with-apptainer',
- 'with-charliecloud',
- 'with-conda',
- 'with-dag',
- 'with-docker',
- 'with-mpi',
- 'with-notification',
- 'with-podman',
- 'with-report',
- 'with-singularity',
- 'with-timeline',
- 'with-tower',
- 'with-trace',
- 'with-weblog',
- 'without-docker',
- 'without-podman',
- 'work-dir'
- ]
- def unexpectedParams = []
-
- // Collect expected parameters from the schema
- def expectedParams = []
- def enums = [:]
- for (group in schemaParams) {
- for (p in group.value['properties']) {
- expectedParams.push(p.key)
- if (group.value['properties'][p.key].containsKey('enum')) {
- enums[p.key] = group.value['properties'][p.key]['enum']
- }
- }
- }
-
- for (specifiedParam in params.keySet()) {
- // nextflow params
- if (nf_params.contains(specifiedParam)) {
- log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'"
- has_error = true
- }
- // unexpected params
- def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params'
- def expectedParamsLowerCase = expectedParams.collect{ it.replace("-", "").toLowerCase() }
- def specifiedParamLowerCase = specifiedParam.replace("-", "").toLowerCase()
- def isCamelCaseBug = (specifiedParam.contains("-") && !expectedParams.contains(specifiedParam) && expectedParamsLowerCase.contains(specifiedParamLowerCase))
- if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam) && !isCamelCaseBug) {
- // Temporarily remove camelCase/camel-case params #1035
- def unexpectedParamsLowerCase = unexpectedParams.collect{ it.replace("-", "").toLowerCase()}
- if (!unexpectedParamsLowerCase.contains(specifiedParamLowerCase)){
- unexpectedParams.push(specifiedParam)
- }
- }
- }
-
- //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~//
- // Validate parameters against the schema
- InputStream input_stream = new File(getSchemaPath(workflow, schema_filename=schema_filename)).newInputStream()
- JSONObject raw_schema = new JSONObject(new JSONTokener(input_stream))
-
- // Remove anything that's in params.schema_ignore_params
- raw_schema = removeIgnoredParams(raw_schema, params)
-
- Schema schema = SchemaLoader.load(raw_schema)
-
- // Clean the parameters
- def cleanedParams = cleanParameters(params)
-
- // Convert to JSONObject
- def jsonParams = new JsonBuilder(cleanedParams)
- JSONObject params_json = new JSONObject(jsonParams.toString())
-
- // Validate
- try {
- schema.validate(params_json)
- } catch (ValidationException e) {
- println ''
- log.error 'ERROR: Validation of pipeline parameters failed!'
- JSONObject exceptionJSON = e.toJSON()
- printExceptions(exceptionJSON, params_json, log, enums)
- println ''
- has_error = true
- }
-
- // Check for unexpected parameters
- if (unexpectedParams.size() > 0) {
- Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
- println ''
- def warn_msg = 'Found unexpected parameters:'
- for (unexpectedParam in unexpectedParams) {
- warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}"
- }
- log.warn warn_msg
- log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}"
- println ''
- }
-
- if (has_error) {
- Nextflow.error('Exiting!')
- }
- }
-
- //
- // Beautify parameters for --help
- //
- public static String paramsHelp(workflow, params, command, schema_filename='nextflow_schema.json') {
- Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
- Integer num_hidden = 0
- String output = ''
- output += 'Typical pipeline command:\n\n'
- output += " ${colors.cyan}${command}${colors.reset}\n\n"
- Map params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
- Integer max_chars = paramsMaxChars(params_map) + 1
- Integer desc_indent = max_chars + 14
- Integer dec_linewidth = 160 - desc_indent
- for (group in params_map.keySet()) {
- Integer num_params = 0
- String group_output = colors.underlined + colors.bold + group + colors.reset + '\n'
- def group_params = params_map.get(group) // This gets the parameters of that particular group
- for (param in group_params.keySet()) {
- if (group_params.get(param).hidden && !params.show_hidden_params) {
- num_hidden += 1
- continue;
- }
- def type = '[' + group_params.get(param).type + ']'
- def description = group_params.get(param).description
- def defaultValue = group_params.get(param).default != null ? " [default: " + group_params.get(param).default.toString() + "]" : ''
- def description_default = description + colors.dim + defaultValue + colors.reset
- // Wrap long description texts
- // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap
- if (description_default.length() > dec_linewidth){
- List olines = []
- String oline = "" // " " * indent
- description_default.split(" ").each() { wrd ->
- if ((oline.size() + wrd.size()) <= dec_linewidth) {
- oline += wrd + " "
- } else {
- olines += oline
- oline = wrd + " "
- }
- }
- olines += oline
- description_default = olines.join("\n" + " " * desc_indent)
- }
- group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n'
- num_params += 1
- }
- group_output += '\n'
- if (num_params > 0){
- output += group_output
- }
- }
- if (num_hidden > 0){
- output += colors.dim + "!! Hiding $num_hidden params, use --show_hidden_params to show them !!\n" + colors.reset
- }
- output += NfcoreTemplate.dashedLine(params.monochrome_logs)
- return output
- }
-
- //
- // Groovy Map summarising parameters/workflow options used by the pipeline
- //
- public static LinkedHashMap paramsSummaryMap(workflow, params, schema_filename='nextflow_schema.json') {
- // Get a selection of core Nextflow workflow options
- def Map workflow_summary = [:]
- if (workflow.revision) {
- workflow_summary['revision'] = workflow.revision
- }
- workflow_summary['runName'] = workflow.runName
- if (workflow.containerEngine) {
- workflow_summary['containerEngine'] = workflow.containerEngine
- }
- if (workflow.container) {
- workflow_summary['container'] = workflow.container
- }
- workflow_summary['launchDir'] = workflow.launchDir
- workflow_summary['workDir'] = workflow.workDir
- workflow_summary['projectDir'] = workflow.projectDir
- workflow_summary['userName'] = workflow.userName
- workflow_summary['profile'] = workflow.profile
- workflow_summary['configFiles'] = workflow.configFiles.join(', ')
-
- // Get pipeline parameters defined in JSON Schema
- def Map params_summary = [:]
- def params_map = paramsLoad(getSchemaPath(workflow, schema_filename=schema_filename))
- for (group in params_map.keySet()) {
- def sub_params = new LinkedHashMap()
- def group_params = params_map.get(group) // This gets the parameters of that particular group
- for (param in group_params.keySet()) {
- if (params.containsKey(param)) {
- def params_value = params.get(param)
- def schema_value = group_params.get(param).default
- def param_type = group_params.get(param).type
- if (schema_value != null) {
- if (param_type == 'string') {
- if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) {
- def sub_string = schema_value.replace('\$projectDir', '')
- sub_string = sub_string.replace('\${projectDir}', '')
- if (params_value.contains(sub_string)) {
- schema_value = params_value
- }
- }
- if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) {
- def sub_string = schema_value.replace('\$params.outdir', '')
- sub_string = sub_string.replace('\${params.outdir}', '')
- if ("${params.outdir}${sub_string}" == params_value) {
- schema_value = params_value
- }
- }
- }
- }
-
- // We have a default in the schema, and this isn't it
- if (schema_value != null && params_value != schema_value) {
- sub_params.put(param, params_value)
- }
- // No default in the schema, and this isn't empty
- else if (schema_value == null && params_value != "" && params_value != null && params_value != false) {
- sub_params.put(param, params_value)
- }
- }
- }
- params_summary.put(group, sub_params)
- }
- return [ 'Core Nextflow options' : workflow_summary ] << params_summary
- }
-
- //
- // Beautify parameters for summary and return as string
- //
- public static String paramsSummaryLog(workflow, params) {
- Map colors = NfcoreTemplate.logColours(params.monochrome_logs)
- String output = ''
- def params_map = paramsSummaryMap(workflow, params)
- def max_chars = paramsMaxChars(params_map)
- for (group in params_map.keySet()) {
- def group_params = params_map.get(group) // This gets the parameters of that particular group
- if (group_params) {
- output += colors.bold + group + colors.reset + '\n'
- for (param in group_params.keySet()) {
- output += " " + colors.blue + param.padRight(max_chars) + ": " + colors.green + group_params.get(param) + colors.reset + '\n'
- }
- output += '\n'
- }
- }
- output += "!! Only displaying parameters that differ from the pipeline defaults !!\n"
- output += NfcoreTemplate.dashedLine(params.monochrome_logs)
- return output
- }
-
- //
- // Loop over nested exceptions and print the causingException
- //
- private static void printExceptions(ex_json, params_json, log, enums, limit=5) {
- def causingExceptions = ex_json['causingExceptions']
- if (causingExceptions.length() == 0) {
- def m = ex_json['message'] =~ /required key \[([^\]]+)\] not found/
- // Missing required param
- if (m.matches()) {
- log.error "* Missing required parameter: --${m[0][1]}"
- }
- // Other base-level error
- else if (ex_json['pointerToViolation'] == '#') {
- log.error "* ${ex_json['message']}"
- }
- // Error with specific param
- else {
- def param = ex_json['pointerToViolation'] - ~/^#\//
- def param_val = params_json[param].toString()
- if (enums.containsKey(param)) {
- def error_msg = "* --${param}: '${param_val}' is not a valid choice (Available choices"
- if (enums[param].size() > limit) {
- log.error "${error_msg} (${limit} of ${enums[param].size()}): ${enums[param][0..limit-1].join(', ')}, ... )"
- } else {
- log.error "${error_msg}: ${enums[param].join(', ')})"
- }
- } else {
- log.error "* --${param}: ${ex_json['message']} (${param_val})"
- }
- }
- }
- for (ex in causingExceptions) {
- printExceptions(ex, params_json, log, enums)
- }
- }
-
- //
- // Remove an element from a JSONArray
- //
- private static JSONArray removeElement(json_array, element) {
- def list = []
- int len = json_array.length()
- for (int i=0;i
- if(raw_schema.keySet().contains('definitions')){
- raw_schema.definitions.each { definition ->
- for (key in definition.keySet()){
- if (definition[key].get("properties").keySet().contains(ignore_param)){
- // Remove the param to ignore
- definition[key].get("properties").remove(ignore_param)
- // If the param was required, change this
- if (definition[key].has("required")) {
- def cleaned_required = removeElement(definition[key].required, ignore_param)
- definition[key].put("required", cleaned_required)
- }
- }
- }
- }
- }
- if(raw_schema.keySet().contains('properties') && raw_schema.get('properties').keySet().contains(ignore_param)) {
- raw_schema.get("properties").remove(ignore_param)
- }
- if(raw_schema.keySet().contains('required') && raw_schema.required.contains(ignore_param)) {
- def cleaned_required = removeElement(raw_schema.required, ignore_param)
- raw_schema.put("required", cleaned_required)
- }
- }
- return raw_schema
- }
-
- //
- // Clean and check parameters relative to Nextflow native classes
- //
- private static Map cleanParameters(params) {
- def new_params = params.getClass().newInstance(params)
- for (p in params) {
- // remove anything evaluating to false
- if (!p['value']) {
- new_params.remove(p.key)
- }
- // Cast MemoryUnit to String
- if (p['value'].getClass() == nextflow.util.MemoryUnit) {
- new_params.replace(p.key, p['value'].toString())
- }
- // Cast Duration to String
- if (p['value'].getClass() == nextflow.util.Duration) {
- new_params.replace(p.key, p['value'].toString().replaceFirst(/d(?!\S)/, "day"))
- }
- // Cast LinkedHashMap to String
- if (p['value'].getClass() == LinkedHashMap) {
- new_params.replace(p.key, p['value'].toString())
- }
- }
- return new_params
- }
-
- //
- // This function tries to read a JSON params file
- //
- private static LinkedHashMap paramsLoad(String json_schema) {
- def params_map = new LinkedHashMap()
- try {
- params_map = paramsRead(json_schema)
- } catch (Exception e) {
- println "Could not read parameters settings from JSON. $e"
- params_map = new LinkedHashMap()
- }
- return params_map
- }
-
- //
- // Method to actually read in JSON file using Groovy.
- // Group (as Key), values are all parameters
- // - Parameter1 as Key, Description as Value
- // - Parameter2 as Key, Description as Value
- // ....
- // Group
- // -
- private static LinkedHashMap paramsRead(String json_schema) throws Exception {
- def json = new File(json_schema).text
- def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions')
- def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties')
- /* Tree looks like this in nf-core schema
- * definitions <- this is what the first get('definitions') gets us
- group 1
- title
- description
- properties
- parameter 1
- type
- description
- parameter 2
- type
- description
- group 2
- title
- description
- properties
- parameter 1
- type
- description
- * properties <- parameters can also be ungrouped, outside of definitions
- parameter 1
- type
- description
- */
-
- // Grouped params
- def params_map = new LinkedHashMap()
- schema_definitions.each { key, val ->
- def Map group = schema_definitions."$key".properties // Gets the property object of the group
- def title = schema_definitions."$key".title
- def sub_params = new LinkedHashMap()
- group.each { innerkey, value ->
- sub_params.put(innerkey, value)
- }
- params_map.put(title, sub_params)
- }
-
- // Ungrouped params
- def ungrouped_params = new LinkedHashMap()
- schema_properties.each { innerkey, value ->
- ungrouped_params.put(innerkey, value)
- }
- params_map.put("Other parameters", ungrouped_params)
-
- return params_map
- }
-
- //
- // Get maximum number of characters across all parameter names
- //
- private static Integer paramsMaxChars(params_map) {
- Integer max_chars = 0
- for (group in params_map.keySet()) {
- def group_params = params_map.get(group) // This gets the parameters of that particular group
- for (param in group_params.keySet()) {
- if (param.size() > max_chars) {
- max_chars = param.size()
- }
- }
- }
- return max_chars
- }
-}
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 25a0a74a..01b8653d 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -3,6 +3,7 @@
//
import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
class NfcoreTemplate {
@@ -128,7 +129,7 @@ class NfcoreTemplate {
def email_html = html_template.toString()
// Render the sendmail template
- def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
+ def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
def sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
@@ -222,6 +223,21 @@ class NfcoreTemplate {
}
}
+ //
+ // Dump pipeline parameters in a json file
+ //
+ public static void dump_parameters(workflow, params) {
+ def output_d = new File("${params.outdir}/pipeline_info/")
+ if (!output_d.exists()) {
+ output_d.mkdirs()
+ }
+
+ def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+ def output_pf = new File(output_d, "params_${timestamp}.json")
+ def jsonStr = JsonOutput.toJson(params)
+ output_pf.text = JsonOutput.prettyPrint(jsonStr)
+ }
+
//
// Print pipeline summary on completion
//
diff --git a/lib/WorkflowAirrflow.groovy b/lib/WorkflowAirrflow.groovy
index 800936b4..9b1c3b97 100755
--- a/lib/WorkflowAirrflow.groovy
+++ b/lib/WorkflowAirrflow.groovy
@@ -40,14 +40,56 @@ class WorkflowAirrflow {
return yaml_file_text
}
- public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) {
+ //
+ // Generate methods description for MultiQC
+ //
+
+ public static String toolCitationText(params) {
+
+ // TODO Optionally add in-text citation tools to this list.
+ // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
+ // Uncomment function in methodsDescriptionText to render in MultiQC report
+ def citation_text = [
+ "Tools used in the workflow included:",
+ "FastQC (Andrews 2010),",
+ "MultiQC (Ewels et al. 2016)",
+ "."
+ ].join(' ').trim()
+
+ return citation_text
+ }
+
+ public static String toolBibliographyText(params) {
+
+ // TODO Optionally add bibliographic entries to this list.
+ // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Author (2023) Pub name, Journal, DOI" : "",
+ // Uncomment function in methodsDescriptionText to render in MultiQC report
+ def reference_text = [
+ "Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).",
+ "Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354"
+ ].join(' ').trim()
+
+ return reference_text
+ }
+
+ public static String methodsDescriptionText(run_workflow, mqc_methods_yaml, params) {
// Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file
def meta = [:]
meta.workflow = run_workflow.toMap()
meta['manifest_map'] = run_workflow.manifest.toMap()
- meta['doi_text'] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : ''
- meta['nodoi_text'] = meta.manifest_map.doi ? '' : 'If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. '
+ // Pipeline DOI
+ meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : ""
+ meta["nodoi_text"] = meta.manifest_map.doi ? "": "If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used. "
+
+ // Tool references
+ meta["tool_citations"] = ""
+ meta["tool_bibliography"] = ""
+
+ // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
+ //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+ //meta["tool_bibliography"] = toolBibliographyText(params)
+
def methods_text = mqc_methods_yaml.text
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index 5342cbb3..538ea8a4 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -19,40 +19,11 @@ class WorkflowMain {
" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
}
- //
- // Generate help string
- //
- public static String help(workflow, params) {
- def command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.tsv --cprimers CPrimers.fasta --vprimers VPrimers.fasta --umi_length 12 --loci ig"
- def help_string = ''
- help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
- help_string += NfcoreSchema.paramsHelp(workflow, params, command)
- help_string += '\n' + citation(workflow) + '\n'
- help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
- return help_string
- }
-
- //
- // Generate parameter summary log string
- //
- public static String paramsSummaryLog(workflow, params) {
- def summary_log = ''
- summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
- summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
- summary_log += '\n' + citation(workflow) + '\n'
- summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
- return summary_log
- }
//
// Validate parameters and print summary to screen
//
public static void initialise(workflow, params, log) {
- // Print help to screen if required
- if (params.help) {
- log.info help(workflow, params)
- System.exit(0)
- }
// Print workflow version and exit on --version
if (params.version) {
@@ -61,14 +32,6 @@ class WorkflowMain {
System.exit(0)
}
- // Print parameter summary log to screen
- log.info paramsSummaryLog(workflow, params)
-
- // Validate workflow parameters via the JSON schema
- if (params.validate_params) {
- NfcoreSchema.validateParameters(workflow, params, log)
- }
-
// Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log)
diff --git a/main.nf b/main.nf
index 2c213e4b..095f148f 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,23 @@ nextflow.enable.dsl = 2
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
+// Commented out as taking too long for big samplesheets
+//include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+
+// Print help message if needed
+if (params.help) {
+ def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+ def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+ def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+ log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
+ System.exit(0)
+}
+
+// Validate input parameters
+//if (params.validate_params) {
+// validateParameters()
+//}
+
WorkflowMain.initialise(workflow, params, log)
/*
diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf
index 9621d685..0ba78193 100644
--- a/modules/local/airrflow_report/airrflow_report.nf
+++ b/modules/local/airrflow_report/airrflow_report.nf
@@ -2,10 +2,12 @@ process AIRRFLOW_REPORT {
tag "${meta.id}"
label 'process_high'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tab) // sequence tsv table in AIRR format
diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf
index 2257913f..6880de53 100644
--- a/modules/local/enchantr/collapse_duplicates.nf
+++ b/modules/local/enchantr/collapse_duplicates.nf
@@ -4,10 +4,12 @@ process COLLAPSE_DUPLICATES {
label 'process_long_parallelized'
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ]
diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf
index 7321603a..c127bbc0 100644
--- a/modules/local/enchantr/define_clones.nf
+++ b/modules/local/enchantr/define_clones.nf
@@ -21,10 +21,12 @@ process DEFINE_CLONES {
label 'process_long_parallelized'
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format
@@ -54,6 +56,7 @@ process DEFINE_CLONES {
'imgt_db'='${imgt_base}', \\
'species'='auto', \\
'cloneby'='${params.cloneby}', \\
+ 'outputby'='${params.cloneby}',
'force'=FALSE, \\
'threshold'=${thr}, \\
'singlecell'='${params.singlecell}','outdir'=getwd(), \\
diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf
index 003c2126..6cdc2fa5 100644
--- a/modules/local/enchantr/detect_contamination.nf
+++ b/modules/local/enchantr/detect_contamination.nf
@@ -5,10 +5,12 @@ process DETECT_CONTAMINATION {
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
path(tabs)
diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf
index 2e398f58..51930bb9 100644
--- a/modules/local/enchantr/dowser_lineages.nf
+++ b/modules/local/enchantr/dowser_lineages.nf
@@ -21,10 +21,12 @@ process DOWSER_LINEAGES {
label 'process_long_parallelized'
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tabs)
diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf
index 32ff652e..06df734c 100644
--- a/modules/local/enchantr/find_threshold.nf
+++ b/modules/local/enchantr/find_threshold.nf
@@ -21,10 +21,12 @@ process FIND_THRESHOLD {
label 'process_long_parallelized'
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
@@ -36,8 +38,8 @@ process FIND_THRESHOLD {
// tuple val(meta), path("*threshold-pass.tsv"), emit: tab // sequence tsv in AIRR format
path("*_command_log.txt"), emit: logs //process logs
path "*_report"
- path "*_threshold-summary.tsv", emit: threshold_summary
- path "*_threshold-mean.tsv", emit: mean_threshold
+ path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary, optional:true
+ path "all_reps_dist_report/tables/*_threshold-mean.tsv", emit: mean_threshold
path "versions.yml", emit: versions
script:
diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf
index 41467ecb..2489362e 100644
--- a/modules/local/enchantr/remove_chimeric.nf
+++ b/modules/local/enchantr/remove_chimeric.nf
@@ -5,10 +5,12 @@ process REMOVE_CHIMERIC {
label 'immcantation'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf
index c9a2052c..b43e1c35 100644
--- a/modules/local/enchantr/report_file_size.nf
+++ b/modules/local/enchantr/report_file_size.nf
@@ -6,10 +6,12 @@ process REPORT_FILE_SIZE {
label 'immcantation'
label 'process_single'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
path logs
diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf
index 3275c523..5f1190e1 100644
--- a/modules/local/enchantr/single_cell_qc.nf
+++ b/modules/local/enchantr/single_cell_qc.nf
@@ -20,10 +20,12 @@ process SINGLE_CELL_QC {
label 'immcantation'
label 'process_medium'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
path(tabs)
diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf
index fd6bd345..d87b27b2 100644
--- a/modules/local/enchantr/validate_input.nf
+++ b/modules/local/enchantr/validate_input.nf
@@ -6,10 +6,12 @@ process VALIDATE_INPUT {
label 'immcantation'
label 'process_single'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
file samplesheet
diff --git a/modules/local/presto/presto_buildconsensus.nf b/modules/local/presto/presto_buildconsensus.nf
index d5e92621..6f5d9b20 100644
--- a/modules/local/presto/presto_buildconsensus.nf
+++ b/modules/local/presto/presto_buildconsensus.nf
@@ -20,11 +20,14 @@ process PRESTO_BUILDCONSENSUS {
path "versions.yml" , emit: versions
script:
- def barcode_field = params.cluster_sets ? "CLUSTER" : "BARCODE"
+ def barcode_field = params.cluster_sets ? 'CLUSTER' : 'BARCODE'
+ def args = task.ext.args ?: ''
+ def args2 = task.ext.args2 ?: ''
+ def args3 = task.ext.args3 ?: ''
"""
- BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
- BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons $params.primer_consensus --maxerror $params.buildconsensus_maxerror --maxgap $params.buildconsensus_maxgap --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
- ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT
+ BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt
+ BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --pf PRIMER --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args2} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt
+ ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ${args3}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf
index f24433e2..b6c817a1 100644
--- a/modules/local/reveal/add_meta_to_tab.nf
+++ b/modules/local/reveal/add_meta_to_tab.nf
@@ -3,10 +3,12 @@ process ADD_META_TO_TAB {
label 'immcantation'
label 'process_single'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
cache 'deep' // Without 'deep' this process would run when using -resume
diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf
index 841fbba9..fa312ece 100644
--- a/modules/local/reveal/filter_junction_mod3.nf
+++ b/modules/local/reveal/filter_junction_mod3.nf
@@ -3,10 +3,12 @@ process FILTER_JUNCTION_MOD3 {
label 'immcantation'
label 'process_single'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf
index a649caef..202840a4 100644
--- a/modules/local/reveal/filter_quality.nf
+++ b/modules/local/reveal/filter_quality.nf
@@ -3,10 +3,12 @@ process FILTER_QUALITY {
label 'immcantation'
label 'process_single'
- conda "bioconda::r-enchantr=0.1.3"
+ if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+ error "nf-core/airrflow currently does not support Conda. Please use a container profile instead."
+ }
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/r-enchantr:0.1.3--r42hdfd78af_0':
- 'biocontainers/r-enchantr:0.1.3--r42hdfd78af_0' }"
+ 'docker.io/immcantation/airrflow:devel':
+ 'docker.io/immcantation/airrflow:devel' }"
input:
tuple val(meta), path(tab) // sequence tsv in AIRR format
diff --git a/nextflow.config b/nextflow.config
index 77d8ef57..c4d958c6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -79,9 +79,10 @@ params {
singlecell = 'single_cell'
clonal_threshold = 'auto'
skip_all_clones_report = false
+ skip_report_threshold = false
// tree lineage options
- igphyml="/usr/local/bin/igphyml"
+ igphyml="/usr/local/share/igphyml/src/igphyml"
skip_lineage = false
// -----------------------
@@ -111,7 +112,6 @@ params {
// Boilerplate options
outdir = null
- tracedir = "${params.outdir}/pipeline_info"
publish_dir_mode = 'copy'
email = null
email_on_fail = null
@@ -120,17 +120,15 @@ params {
hook_url = null
help = false
version = false
- validate_params = true
- show_hidden_params = false
- schema_ignore_params = 'genomes'
// Config options
+ config_profile_name = null
+ config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
- config_profile_description = null
config_profile_contact = null
config_profile_url = null
- config_profile_name = null
+
// Max resource options
// Defaults only, expecting to be overwritten
@@ -138,6 +136,13 @@ params {
max_cpus = 16
max_time = '240.h'
+ // Schema validation default options
+ validationFailUnrecognisedParams = false
+ validationLenientMode = false
+ validationSchemaIgnoreParams = 'genomes'
+ validationShowHiddenParams = false
+ validate_params = true
+
}
// Load base.config by default for all pipelines
@@ -157,14 +162,11 @@ try {
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config")
// }
-docker.registry = 'quay.io'
-podman.registry = 'quay.io'
-
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
- cleanup = false
+ cleanup = false
}
conda {
conda.enabled = true
@@ -265,6 +267,18 @@ profiles {
test_igblast { includeConfig 'conf/test_igblast.config' }
}
+// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
+// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
+// Set to your registry if you have a mirror of containers
+apptainer.registry = 'quay.io'
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+singularity.registry = 'quay.io'
+
+// Nextflow plugins
+plugins {
+ id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
@@ -272,7 +286,6 @@ if (!params.igenomes_ignore) {
} else {
params.genomes = [:]
}
-
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
@@ -281,6 +294,8 @@ env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
+ R_LIBS_SITE = "NULL"
+ R_LIBS_USER = "NULL"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
@@ -290,19 +305,19 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
- file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
- file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
- file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
+ file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
- file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
+ file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
@@ -311,7 +326,7 @@ manifest {
homePage = 'https://github.com/nf-core/airrflow'
description = """B and T cell repertoire analysis pipeline with the Immcantation framework."""
mainScript = 'main.nf'
- nextflowVersion = '!>=22.10.1'
+ nextflowVersion = '!>=23.04.0'
version = '3.2.0dev'
doi = '10.5281/zenodo.2642009'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e6a3365e..e1e77e77 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -14,10 +14,14 @@
"properties": {
"input": {
"type": "string",
- "mimetype": "text/tsv",
- "fa_icon": "fas fa-table",
- "description": "Path to a tsv file providing paths to the fastq files for each sample and the necessary metadata for the analysis.",
- "help_text": "The input file includes important sample metadata and the path to the R1 and R2 fastq files, and index read file (I), if available. Please check the usage docs on information on how to create the input samplesheet."
+ "format": "file-path",
+ "exists": true,
+ "mimetype": "text/csv",
+ "pattern": "^\\S+\\.tsv$",
+ "schema": "assets/schema_input.json",
+ "description": "Path to comma-separated file containing information about the samples in the experiment.",
+ "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/airrflow/usage#samplesheet-input).",
+ "fa_icon": "fas fa-file-csv"
},
"mode": {
"type": "string",
@@ -364,6 +368,11 @@
"type": "boolean",
"description": "Skip report of EnchantR DefineClones for all samples together.",
"fa_icon": "fas fa-angle-double-right"
+ },
+ "skip_report_threshold": {
+ "type": "boolean",
+ "description": "Skip report of EnchantR FindThreshold for all samples together.",
+ "fa_icon": "fas fa-angle-double-right"
}
},
"help_text": "By default, the pipeline will define clones for each of the samples, as two sequences having the same V-gene assignment, C-gene assignment, J-gene assignment, and junction length. Additionally, the similarity of the CDR3 sequences will be assessed by Hamming distances. \n\nA distance threshold for determining if two sequences come from the same clone or not is automatically determined by the process find threshold. Alternatively, a hamming distance threshold can be manually set by setting the `--clonal_threshold` parameter.",
@@ -514,7 +523,7 @@
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
- "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
+ "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
@@ -531,12 +540,14 @@
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
+ "default": false,
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
+ "default": false,
"hidden": true
},
"publish_dir_mode": {
@@ -560,6 +571,7 @@
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
+ "default": false,
"hidden": true
},
"multiqc_title": {
@@ -579,6 +591,7 @@
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
+ "default": false,
"hidden": true
},
"hook_url": {
@@ -590,6 +603,7 @@
},
"multiqc_config": {
"type": "string",
+ "format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
@@ -605,13 +619,6 @@
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
- "tracedir": {
- "type": "string",
- "description": "Directory to keep pipeline Nextflow logs and reports.",
- "default": "${params.outdir}/pipeline_info",
- "fa_icon": "fas fa-cogs",
- "hidden": true
- },
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
@@ -619,12 +626,29 @@
"fa_icon": "fas fa-check-square",
"hidden": true
},
- "show_hidden_params": {
+ "validationShowHiddenParams": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
+ "default": false,
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
+ },
+ "validationFailUnrecognisedParams": {
+ "type": "boolean",
+ "fa_icon": "far fa-check-circle",
+ "description": "Validation of parameters fails when an unrecognised parameter is found.",
+ "default": false,
+ "hidden": true,
+ "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
+ },
+ "validationLenientMode": {
+ "type": "boolean",
+ "fa_icon": "far fa-check-circle",
+ "description": "Validation of parameters in lenient more.",
+ "default": false,
+ "hidden": true,
+ "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
}
}
}
diff --git a/subworkflows/local/clonal_analysis.nf b/subworkflows/local/clonal_analysis.nf
index ff4afacf..b4c413f6 100644
--- a/subworkflows/local/clonal_analysis.nf
+++ b/subworkflows/local/clonal_analysis.nf
@@ -51,13 +51,14 @@ workflow CLONAL_ANALYSIS {
.dump(tag: 'ch_find_threshold_samplesheet')
.collectFile(name: 'find_threshold_samplesheet.txt', newLine: true)
- REPORT_THRESHOLD (
- ch_find_threshold,
- ch_logo,
- ch_find_threshold_samplesheet
- )
- ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions)
-
+ if (!params.skip_report_threshold){
+ REPORT_THRESHOLD (
+ ch_find_threshold,
+ ch_logo,
+ ch_find_threshold_samplesheet
+ )
+ ch_versions = ch_versions.mix(REPORT_THRESHOLD.out.versions)
+ }
}
// prepare ch for define clones
diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf
index 74aab699..2984ecba 100644
--- a/workflows/airrflow.nf
+++ b/workflows/airrflow.nf
@@ -1,12 +1,18 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- VALIDATE INPUTS
+ PRINT PARAMS SUMMARY
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
+
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
-// Validate input parameters
WorkflowAirrflow.initialise(params, log)
// Check input path parameters to see if they exist
@@ -28,6 +34,8 @@ if (params.input) {
ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
+ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
// Report files
ch_report_rmd = Channel.fromPath(params.report_rmd, checkIfExists: true)
@@ -229,9 +237,12 @@ workflow AIRRFLOW {
workflow_summary = WorkflowAirrflow.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)
+ methods_description = WorkflowAirrflow.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
+ ch_methods_description = Channel.value(methods_description)
+
ch_multiqc_files = Channel.empty()
- ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
+ ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(ch_fastp_html.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_fastp_json.ifEmpty([]))