diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 1cca9bc0..88675b1a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index ae4285a7..69a2dd8e 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/taxp - [ ] If necessary, also make a PR on the nf-core/taxprofiler _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a061b247..d44aa343 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,7 +42,7 @@ jobs: steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 96ecd903..7b5ad1c7 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index b8bdd214..905c58e4 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -27,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @@ -40,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Check code lints with Black uses: psf/black@stable @@ -71,7 +71,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcements.yml similarity index 100% rename from .github/workflows/release-announcments.yml rename to .github/workflows/release-announcements.yml diff --git a/.gitpod.yml b/.gitpod.yml index 25488dcc..acf72695 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,9 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - + - name: unset JAVA_TOOL_OPTIONS + command: | + unset JAVA_TOOL_OPTIONS vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/README.md b/README.md index 5be8affe..74451a7f 100644 --- a/README.md +++ b/README.md @@ -47,11 +47,8 @@ ## Usage -:::note -If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -with `-profile test` before running the workflow on actual data. -::: +> [!NOTE] +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: @@ -89,11 +86,9 @@ nextflow run nf-core/taxprofiler \ --run_kraken2 --run_metaphlan ``` -:::warning -Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those -provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; -see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). -::: +> [!WARNING] +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/taxprofiler/usage) and the [parameter documentation](https://nf-co.re/taxprofiler/parameters). diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index fa6c4e17..316663b5 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/taxprofiler + This report has been generated by the nf-core/taxprofiler analysis pipeline. For information about how to interpret these results, please see the documentation. diff --git a/assets/slackreport.json b/assets/slackreport.json index d168147d..01c8319d 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": "nf-core/taxprofiler v${version} - ${runName}", + "author_name": "nf-core/taxprofiler ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules.config b/conf/modules.config index 9c269997..b45267be 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -769,7 +769,7 @@ process { } withName: 'MULTIQC' { - ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } publishDir = [ path: { "${params.outdir}/multiqc" }, mode: params.publish_dir_mode, diff --git a/docs/usage.md b/docs/usage.md index a496363e..dc398350 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -44,12 +44,11 @@ This samplesheet is then specified on the command line as follows: The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate different runs FASTQ files of the same sample before performing profiling, when `--perform_runmerging` is supplied. Below is an example for the same sample sequenced across 3 lanes: -```csv +```csv title="samplesheet.csv" sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta 2612,run1,ILLUMINA,2612_run1_R1.fq.gz,, 2612,run2,ILLUMINA,2612_run2_R1.fq.gz,, 2612,run3,ILLUMINA,2612_run3_R1.fq.gz,2612_run3_R2.fq.gz, - ``` :::warning @@ -62,7 +61,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th A final samplesheet file consisting of both single- and paired-end data, as well as long-read FASTA files may look something like the one below. This is for 6 samples, where `2612` has been sequenced twice. -```csv +```csv title="samplesheet.csv" sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta 2611,ERR5766174,ILLUMINA,,,///fasta/ERX5474930_ERR5766174_1.fa.gz 2612,ERR5766176,ILLUMINA,///fastq/ERX5474932_ERR5766176_1.fastq.gz,///fastq/ERX5474932_ERR5766176_2.fastq.gz, diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 01b8653d..e248e4c3 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -4,6 +4,7 @@ import org.yaml.snakeyaml.Yaml import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -141,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -155,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -227,15 +232,14 @@ 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 filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") def jsonStr = JsonOutput.toJson(params) - output_pf.text = JsonOutput.prettyPrint(jsonStr) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() } // diff --git a/modules.json b/modules.json index d220eecd..9f195992 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "adapterremoval": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "5add1e8e11af620c779462936ce8bbcc1abcef2d", "installed_by": ["modules"] }, "bbmap/bbduk": { @@ -52,7 +52,7 @@ }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "diamond/blastx": { @@ -73,12 +73,12 @@ }, "fastqc": { "branch": "master", - "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117", + "git_sha": "617777a807a1770f73deb38c80004bac06807eef", "installed_by": ["modules"] }, "filtlong": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "b4c8ac68ffcdabac3f63aaa5e7420b175e1d8d76", "installed_by": ["modules"] }, "ganon/classify": { @@ -198,7 +198,7 @@ }, "multiqc": { "branch": "master", - "git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "porechop/porechop": { diff --git a/modules/nf-core/adapterremoval/environment.yml b/modules/nf-core/adapterremoval/environment.yml new file mode 100644 index 00000000..1737b14b --- /dev/null +++ b/modules/nf-core/adapterremoval/environment.yml @@ -0,0 +1,7 @@ +name: adapterremoval +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::adapterremoval=2.3.2 diff --git a/modules/nf-core/adapterremoval/main.nf b/modules/nf-core/adapterremoval/main.nf index 29aac1c0..d128d324 100644 --- a/modules/nf-core/adapterremoval/main.nf +++ b/modules/nf-core/adapterremoval/main.nf @@ -2,7 +2,7 @@ process ADAPTERREMOVAL { tag "$meta.id" label 'process_medium' - conda "bioconda::adapterremoval=2.3.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/adapterremoval:2.3.2--hb7ba0dd_0' : 'biocontainers/adapterremoval:2.3.2--hb7ba0dd_0' }" diff --git a/modules/nf-core/adapterremoval/meta.yml b/modules/nf-core/adapterremoval/meta.yml index 77273f60..2deb613b 100644 --- a/modules/nf-core/adapterremoval/meta.yml +++ b/modules/nf-core/adapterremoval/meta.yml @@ -11,7 +11,6 @@ tools: homepage: https://github.com/MikkelSchubert/adapterremoval documentation: https://adapterremoval.readthedocs.io licence: ["GPL v3"] - input: - meta: type: map @@ -26,17 +25,8 @@ input: pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - adapterlist: type: file - description: Optional text file containing list of adapters to look for for removal - with one adapter per line. Otherwise will look for default adapters (see - AdapterRemoval man page), or can be modified to remove user-specified - adapters via ext.args. - + description: Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - singles_truncated: type: file description: | @@ -50,20 +40,13 @@ output: Adapter trimmed FastQ files of reads that did not pass filtering thresholds. pattern: "*.discarded.fastq.gz" - - pair1_truncated: + - paired_truncated: type: file description: | - Adapter trimmed R1 FastQ files of paired-end reads that did not merge - with their respective R2 pair due to long templates. The respective pair - is stored in 'pair2_truncated'. - pattern: "*.pair1.truncated.fastq.gz" - - pair2_truncated: - type: file - description: | - Adapter trimmed R2 FastQ files of paired-end reads that did not merge - with their respective R1 pair due to long templates. The respective pair - is stored in 'pair1_truncated'. - pattern: "*.pair2.truncated.fastq.gz" + Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge + with their respective R{1,2} pair due to long templates. The respective pair + is stored in 'pair{1,2}_truncated'. + pattern: "*.pair{1,2}.truncated.fastq.gz" - collapsed: type: file description: | @@ -76,7 +59,12 @@ output: Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair and were trimmed of adapter due to sufficient overlap. pattern: "*.collapsed.truncated.fastq.gz" - - log: + - paired_interleaved: + type: file + description: | + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads + pattern: "*.paired.fastq.gz" + - settings: type: file description: AdapterRemoval log file pattern: "*.settings" @@ -84,7 +72,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@maxibor" - "@jfy133" +maintainers: + - "@maxibor" + - "@jfy133" diff --git a/modules/nf-core/adapterremoval/tests/main.nf.test b/modules/nf-core/adapterremoval/tests/main.nf.test new file mode 100644 index 00000000..91c07b7e --- /dev/null +++ b/modules/nf-core/adapterremoval/tests/main.nf.test @@ -0,0 +1,120 @@ +nextflow_process { + + name "Test Process ADAPTERREMOVAL" + script "../main.nf" + process "ADAPTERREMOVAL" + + tag "modules" + tag "modules_nfcore" + tag "adapterremoval" + + test("single-end - sarscov2 - [fastq]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true, collapse:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.singles_truncated, + process.out.settings, + process.out.versions).match() }, + ) + } + } + + test("paired-end - sarscov2 - [fastq]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, collapse:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.paired_truncated, + process.out.settings, + process.out.versions).match() }, + { assert process.out.discarded } + ) + } + + } + + test("paired-end collapse - sarscov2 - [fastq]") { + + options "--collapse" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.paired_truncated, + process.out.collapsed, + process.out.settings, + process.out.versions).match() }, + { assert process.out.discarded } + ) + } + + } + + test("paired-end adapterlist - sarscov2 - [fastq]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, collapse:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ] + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt", + checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.paired_truncated, + process.out.settings, + process.out.versions).match() }, + { assert process.out.discarded } + ) + } + + } + +} diff --git a/modules/nf-core/adapterremoval/tests/main.nf.test.snap b/modules/nf-core/adapterremoval/tests/main.nf.test.snap new file mode 100644 index 00000000..f890167a --- /dev/null +++ b/modules/nf-core/adapterremoval/tests/main.nf.test.snap @@ -0,0 +1,124 @@ +{ + "single-end - sarscov2 - [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true, + "collapse": false + }, + "test.truncated.fastq.gz:md5,119d1b1a0a71ca6e080ff7c53ee0b690" + ] + ], + [ + [ + { + "id": "test", + "single_end": true, + "collapse": false + }, + "test.settings:md5,2fd3d5d703b63ba33a83021fccf25f77" + ] + ], + [ + "versions.yml:md5,00bcc9f0b864b96eeee21bc11773ee67" + ] + ], + "timestamp": "2023-12-09T19:19:36.429445996" + }, + "paired-end - sarscov2 - [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false, + "collapse": false + }, + [ + "test.pair1.truncated.fastq.gz:md5,e3da014fbb9b428e952c62e8f0fb6402", + "test.pair2.truncated.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": false, + "collapse": false + }, + "test.settings:md5,b8a451d3981b327f3fdb44f40ba2d6d1" + ] + ], + [ + "versions.yml:md5,00bcc9f0b864b96eeee21bc11773ee67" + ] + ], + "timestamp": "2023-12-09T19:19:42.88672676" + }, + "paired-end collapse - sarscov2 - [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test.pair1.truncated.fastq.gz:md5,e3da014fbb9b428e952c62e8f0fb6402", + "test.pair2.truncated.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" + ] + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.settings:md5,b8a451d3981b327f3fdb44f40ba2d6d1" + ] + ], + [ + "versions.yml:md5,00bcc9f0b864b96eeee21bc11773ee67" + ] + ], + "timestamp": "2023-12-09T19:19:49.299792876" + }, + "paired-end adapterlist - sarscov2 - [fastq]": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false, + "collapse": false + }, + [ + "test.pair1.truncated.fastq.gz:md5,e3da014fbb9b428e952c62e8f0fb6402", + "test.pair2.truncated.fastq.gz:md5,2ebae722295ea66d84075a3b042e2b42" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": false, + "collapse": false + }, + "test.settings:md5,36d47d9b40dbc178167d1ae0274d18f3" + ] + ], + [ + "versions.yml:md5,00bcc9f0b864b96eeee21bc11773ee67" + ] + ], + "timestamp": "2023-12-09T19:19:57.26567964" + } +} \ No newline at end of file diff --git a/modules/nf-core/adapterremoval/tests/tags.yml b/modules/nf-core/adapterremoval/tests/tags.yml new file mode 100644 index 00000000..d3375ec5 --- /dev/null +++ b/modules/nf-core/adapterremoval/tests/tags.yml @@ -0,0 +1,2 @@ +adapterremoval: + - "modules/nf-core/adapterremoval/**" diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 00000000..9b3272bc --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index c9d014b1..f2187611 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=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657de..5f15a5fd 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..b1e1630b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..5f59a936 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml new file mode 100644 index 00000000..1787b38a --- /dev/null +++ b/modules/nf-core/fastqc/environment.yml @@ -0,0 +1,7 @@ +name: fastqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index 249f9064..9e19a74c 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -2,10 +2,10 @@ process FASTQC { tag "$meta.id" label 'process_medium' - conda "bioconda::fastqc=0.11.9" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' : - 'biocontainers/fastqc:0.11.9--0' }" + 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : + 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" input: tuple val(meta), path(reads) @@ -37,7 +37,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ @@ -49,7 +49,7 @@ process FASTQC { cat <<-END_VERSIONS > versions.yml "${task.process}": - fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" ) + fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) END_VERSIONS """ } diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4da5bb5a..ee5507e0 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -50,3 +50,8 @@ authors: - "@grst" - "@ewels" - "@FelixKrueger" +maintainers: + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 3961de60..ad9bc54f 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -1,32 +1,220 @@ nextflow_process { name "Test Process FASTQC" - script "modules/nf-core/fastqc/main.nf" + script "../main.nf" process "FASTQC" + + tag "modules" + tag "modules_nfcore" tag "fastqc" - test("Single-Read") { + test("sarscov2 single-end [fastq]") { when { process { """ input[0] = [ - [ id: 'test', single_end:true ], - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] ] """ } } then { - assert process.success - assert process.out.html.get(0).get(1) ==~ ".*/test_fastqc.html" - assert path(process.out.html.get(0).get(1)).getText().contains("") - assert process.out.zip.get(0).get(1) ==~ ".*/test_fastqc.zip" + assertAll ( + { assert process.success }, + + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 interleaved [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + file(params.test_data['sarscov2']['illumina']['test_interleaved_fastq_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 paired-end [bam]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 multiple [fastq]") { + + when { + process { + """ + input[0] = [ + [id: 'test', single_end: false], // meta map + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test2_2_fastq_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("") }, + { assert path(process.out.html[0][1][1]).text.contains("") }, + { assert path(process.out.html[0][1][2]).text.contains("") }, + { assert path(process.out.html[0][1][3]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 custom_prefix") { + + when { + process { + """ + input[0] = [ + [ id:'mysample', single_end:true ], // meta map + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("") }, + + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id: 'test', single_end:true ], + [ + file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) + ] + ] + """ + } } + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.html.collect { file(it[1]).getName() } + + process.out.zip.collect { file(it[1]).getName() } + + process.out.versions ).match() } + ) + } } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap new file mode 100644 index 00000000..5ef5afbd --- /dev/null +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -0,0 +1,20 @@ +{ + "sarscov2 single-end [fastq] - stub": { + "content": [ + [ + "test.html", + "test.zip", + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-12-29T02:48:05.126117287" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ] + ], + "timestamp": "2023-12-29T02:46:49.507942667" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml new file mode 100644 index 00000000..7834294b --- /dev/null +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -0,0 +1,2 @@ +fastqc: + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/filtlong/environment.yml b/modules/nf-core/filtlong/environment.yml new file mode 100644 index 00000000..0fb7e8b4 --- /dev/null +++ b/modules/nf-core/filtlong/environment.yml @@ -0,0 +1,7 @@ +name: filtlong +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::filtlong=0.2.1 diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf index a377095c..627247fe 100644 --- a/modules/nf-core/filtlong/main.nf +++ b/modules/nf-core/filtlong/main.nf @@ -2,7 +2,7 @@ process FILTLONG { tag "$meta.id" label 'process_low' - conda "bioconda::filtlong=0.2.1" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' : 'biocontainers/filtlong:0.2.1--h9a82719_0' }" @@ -28,7 +28,7 @@ process FILTLONG { $short_reads \\ $args \\ $longreads \\ - 2> ${prefix}.log \\ + 2> >(tee ${prefix}.log >&2) \\ | gzip -n > ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/filtlong/meta.yml b/modules/nf-core/filtlong/meta.yml index 9be850b0..4a0f072a 100644 --- a/modules/nf-core/filtlong/meta.yml +++ b/modules/nf-core/filtlong/meta.yml @@ -11,11 +11,8 @@ tools: - filtlong: description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. homepage: https://anaconda.org/bioconda/filtlong - tool_dev_url: https://github.com/rrwick/Filtlong - licence: ["GPL v3"] - input: - meta: type: map @@ -30,7 +27,6 @@ input: type: file description: fastq file pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - output: - meta: type: map @@ -49,7 +45,9 @@ output: type: file description: Standard error logging file containing summary statistics pattern: "*.log" - authors: - "@d4straub" - "@sofstam" +maintainers: + - "@d4straub" + - "@sofstam" diff --git a/modules/nf-core/filtlong/tests/main.nf.test b/modules/nf-core/filtlong/tests/main.nf.test new file mode 100644 index 00000000..b7d73e79 --- /dev/null +++ b/modules/nf-core/filtlong/tests/main.nf.test @@ -0,0 +1,99 @@ +nextflow_process { + + name "Test Process FILTLONG" + script "../main.nf" + process "FILTLONG" + config "./nextflow.config" + tag "filtlong" + tag "modules" + tag "modules_nfcore" + + test("sarscov2 nanopore [fastq]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [], + [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.log.get(0).get(1)).readLines().contains("Scoring long reads")}, + { assert snapshot(process.out.reads).match("nanopore") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + + test("sarscov2 nanopore [fastq] + Illumina single-end [fastq]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ], + [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.log.get(0).get(1)).readLines().contains("Scoring long reads")}, + { assert snapshot(process.out.reads).match("nanopore_illumina_se") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + + test("sarscov2 nanopore [fastq] + Illumina paired-end [fastq]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ], + [ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.log.get(0).get(1)).readLines().contains("Scoring long reads")}, + { assert snapshot(process.out.reads).match("nanopore_illumina_pe") }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + +} diff --git a/modules/nf-core/filtlong/tests/main.nf.test.snap b/modules/nf-core/filtlong/tests/main.nf.test.snap new file mode 100644 index 00000000..49d4bb6c --- /dev/null +++ b/modules/nf-core/filtlong/tests/main.nf.test.snap @@ -0,0 +1,52 @@ +{ + "nanopore": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_lr.fastq.gz:md5,7567d853ada6ac142332619d0b541d76" + ] + ] + ], + "timestamp": "2023-12-11T14:23:36.351509" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,af5988f30157282acdb0ac50ebb4c8cc" + ] + ], + "timestamp": "2023-12-11T14:23:36.372189" + }, + "nanopore_illumina_pe": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_lr.fastq.gz:md5,7567d853ada6ac142332619d0b541d76" + ] + ] + ], + "timestamp": "2023-12-11T14:24:05.202047" + }, + "nanopore_illumina_se": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test_lr.fastq.gz:md5,7567d853ada6ac142332619d0b541d76" + ] + ] + ], + "timestamp": "2023-12-11T14:23:50.607338" + } +} \ No newline at end of file diff --git a/modules/nf-core/filtlong/tests/nextflow.config b/modules/nf-core/filtlong/tests/nextflow.config new file mode 100644 index 00000000..5e4c9fbb --- /dev/null +++ b/modules/nf-core/filtlong/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + ext.args = "--min_length 10" + ext.prefix = "test_lr" + +} diff --git a/modules/nf-core/filtlong/tests/tags.yml b/modules/nf-core/filtlong/tests/tags.yml new file mode 100644 index 00000000..bf2cff9d --- /dev/null +++ b/modules/nf-core/filtlong/tests/tags.yml @@ -0,0 +1,2 @@ +filtlong: + - modules/nf-core/filtlong/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..7625b752 --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 65d7dd0d..1b9f7c43 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=1.15" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : - 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml @@ -41,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..45a9bc35 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +12,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +29,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +51,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 00000000..d0438eda --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,83 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("sarscov2 single-end [fastqc]") { + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("sarscov2 single-end [fastqc] [config]") { + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 00000000..d37e7304 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 00000000..bea6c0d3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index 5ded26e1..5badc199 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,7 +13,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false // MultiQC options @@ -208,6 +208,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -230,16 +231,16 @@ profiles { } 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 + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true @@ -319,7 +320,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -343,6 +344,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true @@ -368,7 +372,7 @@ manifest { description = """Taxonomic classification and profiling of shotgun short- and long-read metagenomic data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.3dev' + version = '1.1.3dev' doi = '10.1101/2023.10.20.563221' }
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow
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