$group
\n" - summary_section += "| Process Name | \\n\\", + " \\ Software | \\nVersion | \\n
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | \\npython | \\n\\", + " \\3.11.7 | \\n
| \\n \\", + " \\ | yaml | \\n5.4.1 | \\n
| TOOL1 | \\ntool1 | \\n\\", + " \\0.11.9 | \\n
| TOOL2 | \\n\\", + " \\tool2 | \\n1.9 | \\n
| Workflow | \\nNextflow | \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] ], - "timestamp": "2023-11-03T14:43:22.157011" + "timestamp": "2024-01-09T23:01:18.710682" } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastavalidator/environment.yml b/modules/nf-core/fastavalidator/environment.yml new file mode 100644 index 00000000..70f346ef --- /dev/null +++ b/modules/nf-core/fastavalidator/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "fastavalidator" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::py_fasta_validator=0.6" diff --git a/modules/nf-core/fastavalidator/main.nf b/modules/nf-core/fastavalidator/main.nf new file mode 100644 index 00000000..ac5470fb --- /dev/null +++ b/modules/nf-core/fastavalidator/main.nf @@ -0,0 +1,62 @@ +process FASTAVALIDATOR { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/py_fasta_validator:0.6--py37h595c7a6_0': + 'biocontainers/py_fasta_validator:0.6--py37h595c7a6_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path('*.success.log') , emit: success_log , optional: true + tuple val(meta), path('*.error.log') , emit: error_log , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + py_fasta_validator \\ + -f $fasta \\ + 2> "${prefix}.error.log" \\ + || echo "Errors from fasta_validate printed to ${prefix}.error.log" + + if [ \$(cat "${prefix}.error.log" | wc -l) -gt 0 ]; then + echo "Validation failed..." + + cat \\ + "${prefix}.error.log" + else + echo "Validation successful..." + + mv \\ + "${prefix}.error.log" \\ + fasta_validate.stderr + + echo "Validation successful..." \\ + > "${prefix}.success.log" + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + py_fasta_validator: \$(py_fasta_validator -v | sed 's/.* version //') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "Validation successful..." \\ + > "${prefix}.success.log" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + py_fasta_validator: \$(py_fasta_validator -v | sed 's/.* version //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/fastavalidator/meta.yml b/modules/nf-core/fastavalidator/meta.yml new file mode 100644 index 00000000..c5c4371c --- /dev/null +++ b/modules/nf-core/fastavalidator/meta.yml @@ -0,0 +1,53 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "fastavalidator" +description: | + "Python C-extension for a simple validator for fasta files. The module emits the validated file or an + error log upon validation failure." +keywords: + - fasta + - validation + - genome +tools: + - fasta_validate: + description: | + "Python C-extension for a simple C code to validate a fasta file. It only checks a few things, + and by default only sets its response via the return code, + so you will need to check that!" + homepage: "https://github.com/linsalrob/py_fasta_validator" + documentation: "https://github.com/linsalrob/py_fasta_validator" + tool_dev_url: "https://github.com/linsalrob/py_fasta_validator" + doi: "10.5281/zenodo.5002710" + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.fasta" +output: + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - success_log: + type: file + description: Log file for successful validation + pattern: "*.success.log" + - error_log: + type: file + description: Log file for failed validation + pattern: "*.error.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@gallvp" +maintainers: + - "@gallvp" diff --git a/modules/nf-core/fastavalidator/tests/main.nf.test b/modules/nf-core/fastavalidator/tests/main.nf.test new file mode 100644 index 00000000..bb8c22cf --- /dev/null +++ b/modules/nf-core/fastavalidator/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process FASTAVALIDATOR" + script "../main.nf" + process "FASTAVALIDATOR" + + tag "modules" + tag "modules_nfcore" + tag "fastavalidator" + + test("sarscov2-fasta-valid") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.success_log != null }, + { assert process.out.error_log == [] }, + { assert path(process.out.success_log.get(0).get(1)).getText().contains("Validation successful...") } + ) + } + + } + + test("sarscov2-gff3-invalid") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.success_log == [] }, + { assert process.out.error_log != null }, + { assert path(process.out.error_log.get(0).get(1)).getText().contains("genome.gff3 does not start with a >") } + ) + } + + } +} diff --git a/modules/nf-core/fastavalidator/tests/main.nf.test.snap b/modules/nf-core/fastavalidator/tests/main.nf.test.snap new file mode 100644 index 00000000..382dee72 --- /dev/null +++ b/modules/nf-core/fastavalidator/tests/main.nf.test.snap @@ -0,0 +1,76 @@ +{ + "sarscov2-fasta-valid": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.success.log:md5,b0b859eda1db5cd43915846e00ebc22c" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7" + ], + "error_log": [ + + ], + "success_log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.success.log:md5,b0b859eda1db5cd43915846e00ebc22c" + ] + ], + "versions": [ + "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7" + ] + } + ], + "timestamp": "2023-11-28T11:23:25.106872" + }, + "sarscov2-gff3-invalid": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.error.log:md5,531d520c0e7767176f743f197f1f87b3" + ] + ], + "2": [ + "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7" + ], + "error_log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.error.log:md5,531d520c0e7767176f743f197f1f87b3" + ] + ], + "success_log": [ + + ], + "versions": [ + "versions.yml:md5,05aa059840b3b4dd6d88bc1e4bf976d7" + ] + } + ], + "timestamp": "2023-11-28T11:23:29.40324" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastavalidator/tests/tags.yml b/modules/nf-core/fastavalidator/tests/tags.yml new file mode 100644 index 00000000..c3c77576 --- /dev/null +++ b/modules/nf-core/fastavalidator/tests/tags.yml @@ -0,0 +1,2 @@ +fastavalidator: + - "modules/nf-core/fastavalidator/**" diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index 9e19a74c..00000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - 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 deleted file mode 100644 index ee5507e0..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@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 deleted file mode 100644 index b9e8f926..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,109 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("Single-Read") { - - when { - params { - outdir = "$outputDir" - } - 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 }, - // 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:|
| File type | Conventional base calls |