Data was processed using nf-core/quantms v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).
+ Data was processed using nf-core/quantms v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
Notes:
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index afd31f93..7568e689 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
report_comment: >
- This report has been generated by the
nf-core/quantms
+ This report has been generated by the
nf-core/quantms
analysis pipeline. For information about how to interpret these results, please see the
-
documentation.
+
documentation.
report_section_order:
pmultiqc:
order: 1
diff --git a/assets/nf-core-quantms_logo_light.png b/assets/nf-core-quantms_logo_light.png
index 71f6dfa4..030a38e8 100644
Binary files a/assets/nf-core-quantms_logo_light.png and b/assets/nf-core-quantms_logo_light.png differ
diff --git a/assets/slackreport.json b/assets/slackreport.json
index 043d02f2..5f7ba081 100644
--- a/assets/slackreport.json
+++ b/assets/slackreport.json
@@ -3,7 +3,7 @@
{
"fallback": "Plain-text summary of the attachment.",
"color": "<% if (success) { %>good<% } else { %>danger<%} %>",
- "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+ "author_name": "nf-core/quantms v${version} - ${runName}",
"author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
"text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
"fields": [
diff --git a/bin/check_samplesheet.py b/bin/check_samplesheet.py
index dd125b4e..2ae0a86f 100755
--- a/bin/check_samplesheet.py
+++ b/bin/check_samplesheet.py
@@ -44,6 +44,28 @@ def print_error(error, context="Line", context_str=""):
sys.exit(1)
+def sniff_format(handle):
+ """
+ Detect the tabular format.
+
+ Args:
+ handle (text file): A handle to a `text file`_ object. The read position is
+ expected to be at the beginning (index 0).
+
+ Returns:
+ csv.Dialect: The detected tabular format.
+
+ .. _text file:
+ https://docs.python.org/3/glossary.html#term-text-file
+
+ """
+ peek = read_head(handle)
+ handle.seek(0)
+ sniffer = csv.Sniffer()
+ dialect = sniffer.sniff(peek)
+ return dialect
+
+
def check_sdrf(check_ms, sdrf):
df = SdrfDataFrame.parse(sdrf)
errors = df.validate(DEFAULT_TEMPLATE)
diff --git a/conf/base.config b/conf/base.config
index 6f9d0207..7648d2cd 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -15,8 +15,8 @@ process {
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 4.h * task.attempt, 'time' ) }
- errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
- maxRetries = 2
+ errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+ maxRetries = 1
maxErrors = '-1'
// Process-specific resource requirements
diff --git a/conf/test_dia.config b/conf/test_dia.config
index b6654bc6..666101ff 100644
--- a/conf/test_dia.config
+++ b/conf/test_dia.config
@@ -20,7 +20,6 @@ params {
max_time = 48.h
outdir = './results_dia'
- tracedir = "${params.outdir}/pipeline_info"
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/dia_ci/PXD026600.sdrf.tsv'
diff --git a/conf/test_full_dia.config b/conf/test_full_dia.config
index 6c4f68f9..1cfdd16d 100644
--- a/conf/test_full_dia.config
+++ b/conf/test_full_dia.config
@@ -20,7 +20,6 @@ params {
max_time = 48.h
outdir = './results_dia_full'
- tracedir = "${params.outdir}/pipeline_info"
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/dia_full/PXD004684.sdrf.tsv'
diff --git a/conf/test_full_lfq.config b/conf/test_full_lfq.config
index b93f1913..fe17eb44 100644
--- a/conf/test_full_lfq.config
+++ b/conf/test_full_lfq.config
@@ -20,7 +20,6 @@ params {
max_time = 48.h
outdir = "./results_lfq_full"
- tracedir = "${params.outdir}/pipeline_info"
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata-aws/lfq_full/PXD001819.sdrf.tsv'
diff --git a/conf/test_full_tmt.config b/conf/test_full_tmt.config
index 99569fbe..d4b8469f 100644
--- a/conf/test_full_tmt.config
+++ b/conf/test_full_tmt.config
@@ -15,7 +15,6 @@ params {
config_profile_description = 'Real full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
outdir = "./results_iso_full"
- tracedir = "${params.outdir}/pipeline_info"
max_cpus = 2
max_memory = 6.GB
diff --git a/conf/test_lfq.config b/conf/test_lfq.config
index 2e280626..cd2480ba 100644
--- a/conf/test_lfq.config
+++ b/conf/test_lfq.config
@@ -20,7 +20,6 @@ params {
max_time = 48.h
outdir = "./results_lfq"
- tracedir = "${params.outdir}/pipeline_info"
// Input data
labelling_type = "label free sample"
diff --git a/conf/test_localize.config b/conf/test_localize.config
index 1129b2c7..3ed7a152 100644
--- a/conf/test_localize.config
+++ b/conf/test_localize.config
@@ -20,7 +20,6 @@ params {
max_time = 1.h
outdir = "./results_localize"
- tracedir = "${params.outdir}/pipeline_info"
// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci_phospho/test_phospho.sdrf'
diff --git a/conf/test_tmt.config b/conf/test_tmt.config
index 489ff442..7184f1a4 100644
--- a/conf/test_tmt.config
+++ b/conf/test_tmt.config
@@ -15,7 +15,6 @@ params {
config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
outdir = "./results_iso"
- tracedir = "${params.outdir}/pipeline_info"
max_cpus = 2
max_memory = 6.GB
diff --git a/docs/usage.md b/docs/usage.md
index 84cc751d..003f6f93 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -33,6 +33,29 @@ work # Directory containing the nextflow working files
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```
+If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
+
+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:
+
+```bash
+nextflow run nf-core/quantms -profile docker -params-file params.yaml
+```
+
+with `params.yaml` containing:
+
+```yaml
+input: './samplesheet.csv'
+outdir: './results/'
+genome: 'GRCh37'
+<...>
+```
+
+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:
@@ -49,6 +72,10 @@ First, go to the [nf-core/quantms releases page](https://github.com/nf-core/quan
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 reproducbility, 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
> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
@@ -57,7 +84,7 @@ This version number will be logged in reports when you run the pipeline, so that
Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments.
-Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Conda) - see below.
+Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
@@ -81,8 +108,10 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
- A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/)
- `charliecloud`
- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
+- `apptainer`
+ - A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
- `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 or Charliecloud.
+ - 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`
@@ -102,102 +131,19 @@ Each step in the pipeline has a default set of requirements for number of CPUs,
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.
-For example, if the nf-core/rnaseq pipeline is failing after multiple re-submissions of the `STAR_ALIGN` process due to an exit code of `137` this would indicate that there is an out of memory issue:
-
-```console
-[62/149eb0] NOTE: Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137) -- Execution is retried (1)
-Error executing process > 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)'
-
-Caused by:
- Process `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)` terminated with an error exit status (137)
-
-Command executed:
- STAR \
- --genomeDir star \
- --readFilesIn WT_REP1_trimmed.fq.gz \
- --runThreadN 2 \
- --outFileNamePrefix WT_REP1. \
-
-
-Command exit status:
- 137
-
-Command output:
- (empty)
-
-Command error:
- .command.sh: line 9: 30 Killed STAR --genomeDir star --readFilesIn WT_REP1_trimmed.fq.gz --runThreadN 2 --outFileNamePrefix WT_REP1.
-Work dir:
- /home/pipelinetest/work/9d/172ca5881234073e8d76f2a19c88fb
-
-Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-```
-
-#### For beginners
-
-A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below.
-
-#### Advanced option on process level
-
-To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN).
-We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`.
-If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9).
-The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements.
-The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB.
-Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB.
-The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections.
-
-```nextflow
-process {
- withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN' {
- memory = 100.GB
- }
-}
-```
-
-> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden.
->
-> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly.
-
-### Updating containers (advanced users)
-
-The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`.
-
-1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19)
-2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags)
-3. Create the custom config accordingly:
-
- - For Docker:
+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.
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'quay.io/biocontainers/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
+### Custom Containers
- - For Singularity:
+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 maybe out of date.
- ```nextflow
- process {
- withName: PANGOLIN {
- container = 'https://depot.galaxyproject.org/singularity/pangolin:3.0.5--pyhdfd78af_0'
- }
- }
- ```
+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.
- - For Conda:
+### Custom Tool Arguments
- ```nextflow
- process {
- withName: PANGOLIN {
- conda = 'bioconda::pangolin=3.0.5'
- }
- }
- ```
+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.
-> **NB:** If you wish to periodically update individual tool-specific results (e.g. Pangolin) generated by the pipeline then you must ensure to keep the `work/` directory otherwise the `-resume` ability of the pipeline will be compromised and it will restart from scratch.
+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
diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy
deleted file mode 100755
index 33cd4f6e..00000000
--- a/lib/NfcoreSchema.groovy
+++ /dev/null
@@ -1,528 +0,0 @@
-//
-// This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template.
-//
-
-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-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) {
- System.exit(1)
- }
- }
-
- //
- // 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."$key".title
- def sub_params = new LinkedHashMap()
- group.each { innerkey, value ->
- sub_params.put(innerkey, value)
- }
- params_map.put(title, sub_params)
- }
-
- // Ungrouped params
- def ungrouped_params = new LinkedHashMap()
- schema_properties.each { innerkey, value ->
- ungrouped_params.put(innerkey, value)
- }
- params_map.put("Other parameters", ungrouped_params)
-
- return params_map
- }
-
- //
- // Get maximum number of characters across all parameter names
- //
- private static Integer paramsMaxChars(params_map) {
- Integer max_chars = 0
- for (group in params_map.keySet()) {
- def group_params = params_map.get(group) // This gets the parameters of that particular group
- for (param in group_params.keySet()) {
- if (param.size() > max_chars) {
- max_chars = param.size()
- }
- }
- }
- return max_chars
- }
-}
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 25a0a74a..408951ae 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -128,7 +128,7 @@ class NfcoreTemplate {
def email_html = html_template.toString()
// Render the sendmail template
- def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
+ def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
def sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
diff --git a/lib/WorkflowMain.groovy b/lib/WorkflowMain.groovy
index db89bb98..0cb27015 100755
--- a/lib/WorkflowMain.groovy
+++ b/lib/WorkflowMain.groovy
@@ -2,6 +2,8 @@
// This file holds several functions specific to the main.nf workflow in the nf-core/quantms pipeline
//
+import nextflow.Nextflow
+
class WorkflowMain {
//
@@ -18,40 +20,11 @@ class WorkflowMain {
" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
}
- //
- // Generate help string
- //
- public static String help(workflow, params, log) {
- def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
- 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, log) {
- 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, log)
- System.exit(0)
- }
// Print workflow version and exit on --version
if (params.version) {
@@ -60,14 +33,6 @@ class WorkflowMain {
System.exit(0)
}
- // Print parameter summary log to screen
- log.info paramsSummaryLog(workflow, params, log)
-
- // 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)
@@ -81,27 +46,12 @@ class WorkflowMain {
// Check input has been provided
if (!params.input) {
- log.error "Please provide an input sdrf to the pipeline e.g. '--input *.sdrf.csv'"
- System.exit(1)
- }
-
- // Check input has been provided
- if (!params.outdir) {
- log.error "Please provide an outdir to the pipeline e.g. '--outdir ./results'"
- System.exit(1)
- }
-
- if (params.tracedir == "null/pipeline_info")
- {
- log.error """Error: Your tracedir is `null/pipeline_info`, this means you probably set outdir in a way that does not affect the default
- `\$params.outdir/pipeline_info` (e.g., by specifying outdir in a profile instead of the commandline or through a `-params-file`.
- Either set outdir in a correct way, or redefine tracedir as well (e.g., in your profile)."""
- System.exit(1)
+ Nextflow.error("Please provide an input sdrf to the pipeline e.g. '--input *.sdrf.csv'")
}
// check fasta database has been provided
if (!params.database) {
- log.error "Please provide an fasta database to the pipeline e.g. '--database *.fasta'"
+ Nextflow.error("Please provide an fasta database to the pipeline e.g. '--database *.fasta'")
}
}
}
diff --git a/lib/WorkflowQuantms.groovy b/lib/WorkflowQuantms.groovy
index 0ae28af2..1bcd9a66 100755
--- a/lib/WorkflowQuantms.groovy
+++ b/lib/WorkflowQuantms.groovy
@@ -1,6 +1,8 @@
//
// This file holds several functions specific to the workflow/quantms.nf in the nf-core/quantms pipeline
//
+
+import nextflow.Nextflow
import groovy.text.SimpleTemplateEngine
class WorkflowQuantms {
@@ -10,8 +12,7 @@ class WorkflowQuantms {
//
public static void initialise(params, log) {
if (!params.database) {
- log.error "database file not specified with e.g. '--database *.fasta' or via a detectable config file."
- System.exit(1)
+ Nextflow.error "database file not specified with e.g. '--database *.fasta' or via a detectable config file."
}
}
@@ -42,15 +43,57 @@ class WorkflowQuantms {
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()
+ // 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
def engine = new SimpleTemplateEngine()
diff --git a/main.nf b/main.nf
index 8b15941a..6db1c8b3 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,22 @@ nextflow.enable.dsl = 2
========================================================================================
*/
+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 ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+ log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
+ System.exit(0)
+}
+
+// Validate input parameters
+if (params.validate_params) {
+ validateParameters()
+}
+
WorkflowMain.initialise(workflow, params, log)
/*
diff --git a/modules.json b/modules.json
index 011ee5f9..9bb0b423 100644
--- a/modules.json
+++ b/modules.json
@@ -7,12 +7,12 @@
"nf-core": {
"custom/dumpsoftwareversions": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
- "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+ "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"installed_by": ["modules"]
}
}
diff --git a/modules/local/openms/epifany/main.nf b/modules/local/openms/epifany/main.nf
index dbae49c7..afc6629c 100644
--- a/modules/local/openms/epifany/main.nf
+++ b/modules/local/openms/epifany/main.nf
@@ -2,8 +2,6 @@ process EPIFANY {
label 'process_medium'
label 'openms'
- publishDir "${params.outdir}"
-
conda "bioconda::openms=2.9.1"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:2.9.1--h135471a_0' :
diff --git a/modules/local/openms/proteomicslfq/main.nf b/modules/local/openms/proteomicslfq/main.nf
index 4c061684..4ebb3fef 100644
--- a/modules/local/openms/proteomicslfq/main.nf
+++ b/modules/local/openms/proteomicslfq/main.nf
@@ -44,7 +44,7 @@ process PROTEOMICSLFQ {
-quantification_method ${params.quantification_method} \\
-targeted_only ${params.targeted_only} \\
-mass_recalibration ${params.mass_recalibration} \\
- -transfer_ids ${params.transfer_ids} \\
+ -transfer_ids ${params.transfer_ids == 'off' ? 'false' : params.transfer_ids} \\
-protein_quantification ${params.protein_quant} \\
-alignment_order ${params.alignment_order} \\
${decoys_present} \\
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 3df21765..800a6099 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
label 'process_single'
// Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
index 60b546a0..c32657de 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: custom_dumpsoftwareversions
description: Custom module used to dump software versions within the nf-core pipeline template
keywords:
- custom
+ - dump
- version
tools:
- custom:
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 68f66bea..4b604749 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,10 +1,10 @@
process MULTIQC {
label 'process_single'
- conda "bioconda::multiqc=1.13"
+ conda "bioconda::multiqc=1.14"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
- 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
- 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
+ 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+ 'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
input:
path multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index ebc29b27..f93b5ee5 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
name: MultiQC
description: Aggregate results from bioinformatics analyses across many samples into a single report
keywords:
@@ -37,7 +38,7 @@ output:
description: MultiQC report file
pattern: "multiqc_report.html"
- data:
- type: dir
+ type: directory
description: MultiQC data dir
pattern: "multiqc_data"
- plots:
diff --git a/nextflow.config b/nextflow.config
index 98ab6da9..18fd81fb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -16,6 +16,9 @@ params {
database = null
acquisition_method = null
+ // Input options
+ input = null
+
// Tools flags
posterior_probabilities = 'percolator'
add_decoys = false
@@ -142,7 +145,7 @@ params {
quantification_method = 'feature_intensity'
targeted_only = true
mass_recalibration = false
- transfer_ids = 'false'
+ transfer_ids = 'off'
alignment_order = 'star'
add_triqler_output = false
quantify_decoys = false
@@ -195,7 +198,6 @@ params {
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
- tracedir = "${params.outdir}/pipeline_info"
email = null
email_on_fail = null
plaintext_email = false
@@ -203,21 +205,17 @@ params {
hook_url = null
help = false
version = false
- validate_params = true
- show_hidden_params = false
- schema_ignore_params = 'modules'
- singularity_pull_docker_container = false
// 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}"
- hostnames = [:]
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
@@ -225,6 +223,13 @@ 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
@@ -237,16 +242,17 @@ try {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
+// Load nf-core/quantms custom profiles from different institutions.
+// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
+// try {
+// includeConfig "${params.custom_config_base}/pipeline/quantms.config"
+// } catch (Exception e) {
+// System.err.println("WARNING: Could not load nf-core/config/quantms profiles: ${params.custom_config_base}/pipeline/quantms.config")
+// }
+
+
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
- ebicluster {
- conda.enabled = true
- docker.enabled = false
- singularity.enabled = false
- conda.createTimeout = '1 h'
- conda.useMamba = true
- process.executor = 'lsf'
- }
conda {
conda.enabled = true
docker.enabled = false
@@ -254,17 +260,6 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
- conda.useMamba = true
- }
- micromamba {
- conda.enabled = true
- conda.useMicromamba = true
- conda.createTimeout = '1 h'
- docker.enabled = false
- singularity.enabled = false
- podman.enabled = false
- shifter.enabled = false
- charliecloud.enabled = false
}
mamba {
conda.enabled = true
@@ -275,14 +270,17 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
+ conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
@@ -290,37 +288,72 @@ profiles {
singularity {
singularity.enabled = true
singularity.autoMounts = true
+ conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
podman {
podman.enabled = true
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
shifter {
shifter.enabled = true
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
+ apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
+ conda.enabled = false
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ apptainer.enabled = false
+ }
+ apptainer {
+ apptainer.enabled = true
+ conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
+ charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 16
executor.memory = 60.GB
}
+ micromamba {
+ conda.enabled = true
+ conda.useMicromamba = true
+ conda.createTimeout = '1 h'
+ docker.enabled = false
+ singularity.enabled = false
+ podman.enabled = false
+ shifter.enabled = false
+ charliecloud.enabled = false
+ }
+ ebicluster {
+ conda.enabled = true
+ docker.enabled = false
+ singularity.enabled = false
+ conda.createTimeout = '1 h'
+ conda.useMamba = true
+ process.executor = 'lsf'
+ }
test { includeConfig 'conf/test_lfq.config' }
test_localize { includeConfig 'conf/test_localize.config' }
test_tmt { includeConfig 'conf/test_tmt.config' }
@@ -331,11 +364,8 @@ profiles {
test_full_dia { includeConfig 'conf/test_full_dia.config' }
test_full { includeConfig 'conf/test_full_lfq.config' }
mambaci { includeConfig 'conf/mambaci.config' }
-}
-// Load module config after profile, so they can depend on overwritten input parameters specific for each profile.
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
+}
// 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.
@@ -354,19 +384,19 @@ 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 {
@@ -375,7 +405,7 @@ manifest {
homePage = 'https://github.com/nf-core/quantms'
description = """Quantitative Mass Spectrometry nf-core workflow"""
mainScript = 'main.nf'
- nextflowVersion = '!>=22.10.1'
+ nextflowVersion = '!>=23.04.0'
version = '1.2.0dev'
doi = '10.5281/zenodo.7754148'
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8470e3d0..12720cbc 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -14,7 +14,10 @@
"properties": {
"input": {
"type": "string",
+ "format": "file-path",
+ "exists": true,
"mimetype": "text/tsv",
+ "pattern": "^\\S+\\.(?:tsv|sdrf)$",
"description": "URI/path to an [SDRF](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) file (.sdrf.tsv) **OR** [OpenMS-style experimental design](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) with paths to spectra files (.tsv)",
"help_text": "Input is specified by using a path or URI to a PRIDE Sample to Data Relation Format file (SDRF), e.g. as part of a submitted and\nannotated PRIDE experiment (see [here](https://github.com/bigbio/proteomics-metadata-standard/tree/master/annotated-projects) for examples). Input files will be downloaded and cached from the URIs specified in the SDRF file.\nAn OpenMS-style experimental design will be generated based on the factor columns of the SDRF. The settings for the\nfollowing parameters will currently be overwritten by the ones specified in the SDRF:\n\n * `fixed_mods`,\n * `variable_mods`,\n * `precursor_mass_tolerance`,\n * `precursor_mass_tolerance_unit`,\n * `fragment_mass_tolerance`,\n * `fragment_mass_tolerance_unit`,\n * `fragment_method`,\n * `enzyme`\n You can also specify an [OpenMS-style experimental design](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html#details) directly (.tsv ending). In this case, the aforementioned parameters have to be specified or defaults will be used.",
"fa_icon": "fas fa-file-csv"
@@ -67,6 +70,10 @@
"properties": {
"database": {
"type": "string",
+ "format": "file-path",
+ "exists": true,
+ "mimetype": "text/fasta",
+ "pattern": "^\\S+\\.(?:fasta|fa)$",
"description": "The `fasta` protein database used during database search. *Note:* For DIA data, it must not contain decoys.",
"fa_icon": "fas fa-file",
"help_text": "Since the database is not included in an SDRF, this parameter always needs to be given to specify the input protein database\nwhen you run the pipeline. Remember to include contaminants (and decoys if not in DIA mode and if not added in the pipeline with [`--add_decoys`](#add_decoys))\n\n```bash\n--database '[path to fasta protein database]'\n```"
@@ -801,9 +808,9 @@
},
"transfer_ids": {
"type": "string",
- "description": "Tries a targeted requantification in files where an ID is missing, based on aggregate properties (i.e. RT) of the features in other aligned files (e.g. 'mean' of RT). (**WARNING:** increased memory consumption and runtime). 'false' turns this feature off. (default: 'false')",
- "default": "false",
- "enum": ["false", "mean"],
+ "description": "Tries a targeted requantification in files where an ID is missing, based on aggregate properties (i.e. RT) of the features in other aligned files (e.g. 'mean' of RT). (**WARNING:** increased memory consumption and runtime). 'off' turns this feature off. (default: 'off')",
+ "default": "off",
+ "enum": ["off", "mean"],
"fa_icon": "fas fa-list-ol"
},
"targeted_only": {
@@ -1115,7 +1122,7 @@
"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'`"
}
@@ -1132,12 +1139,14 @@
"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": {
@@ -1161,6 +1170,7 @@
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
+ "default": false,
"hidden": true
},
"max_multiqc_email_size": {
@@ -1175,6 +1185,7 @@
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
+ "default": false,
"hidden": true
},
"hook_url": {
@@ -1186,6 +1197,7 @@
},
"multiqc_config": {
"type": "string",
+ "format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
@@ -1207,13 +1219,6 @@
"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",
@@ -1221,24 +1226,29 @@
"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."
},
- "singularity_pull_docker_container": {
+ "validationFailUnrecognisedParams": {
"type": "boolean",
- "description": "This parameter force singularity to pull the contain from docker instead of using the singularity image",
+ "fa_icon": "far fa-check-circle",
+ "description": "Validation of parameters fails when an unrecognised parameter is found.",
+ "default": false,
"hidden": true,
- "fa_icon": "fas fa-bacon"
+ "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
- "hostnames": {
- "type": "string",
- "description": "Institutional configs hostname.",
+ "validationLenientMode": {
+ "type": "boolean",
+ "fa_icon": "far fa-check-circle",
+ "description": "Validation of parameters in lenient more.",
+ "default": false,
"hidden": true,
- "fa_icon": "fas fa-users-cog"
+ "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/tower.yml b/tower.yml
new file mode 100644
index 00000000..787aedfe
--- /dev/null
+++ b/tower.yml
@@ -0,0 +1,5 @@
+reports:
+ multiqc_report.html:
+ display: "MultiQC HTML report"
+ samplesheet.csv:
+ display: "Auto-created samplesheet with collated metadata and FASTQ paths"
diff --git a/workflows/quantms.nf b/workflows/quantms.nf
index b9c51946..e65830ec 100644
--- a/workflows/quantms.nf
+++ b/workflows/quantms.nf
@@ -1,21 +1,19 @@
/*
-========================================================================================
- VALIDATE INPUTS
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ PRINT PARAMS SUMMARY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
-// Validate input parameters
-WorkflowQuantms.initialise(params, log)
+def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
+def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
+def summary_params = paramsSummaryMap(workflow)
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
-// Check input path parameters to see if they exist
-def checkPathParamList = [ params.input ]
-for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
+// Print parameter summary log to screen
+log.info logo + paramsSummaryLog(workflow) + citation
-// Check mandatory parameters
-if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
+WorkflowQuantms.initialise(params, log)
/*
========================================================================================
@@ -80,9 +78,12 @@ workflow QUANTMS {
// SUBWORKFLOW: Read in samplesheet, validate and stage input files
//
INPUT_CHECK (
- ch_input
+ file(params.input)
)
ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
+ // TODO: OPTIONAL, you can use nf-validation plugin to create an input channel from the samplesheet with Channel.fromSamplesheet("input")
+ // See the documentation https://nextflow-io.github.io/nf-validation/samplesheets/fromSamplesheet/
+ // ! There is currently no tooling to help you write a sample sheet schema
//
// SUBWORKFLOW: Create input channel
@@ -173,7 +174,7 @@ workflow QUANTMS {
workflow_summary = WorkflowQuantms.paramsSummaryMultiqc(workflow, summary_params)
ch_workflow_summary = Channel.value(workflow_summary)
- methods_description = WorkflowQuantms.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description)
+ methods_description = WorkflowQuantms.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description, params)
ch_methods_description = Channel.value(methods_description)
ch_multiqc_files = Channel.empty()
