From 74b60dd4f46da934e9cf23ce1292584c135b78b0 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Thu, 11 Jan 2024 08:41:37 +0000 Subject: [PATCH] Support input read-sets being paired-end --- bin/check_fetchngs_samplesheet.py | 8 +- modules.json | 5 + modules/nf-core/cat/cat/environment.yml | 7 + modules/nf-core/cat/cat/main.nf | 70 +++++++ modules/nf-core/cat/cat/meta.yml | 36 ++++ modules/nf-core/cat/cat/tests/main.nf.test | 179 ++++++++++++++++++ .../nf-core/cat/cat/tests/main.nf.test.snap | 121 ++++++++++++ .../cat/tests/nextflow_unzipped_zipped.config | 6 + .../cat/tests/nextflow_zipped_unzipped.config | 8 + modules/nf-core/cat/cat/tests/tags.yml | 2 + subworkflows/local/input_check.nf | 18 +- 11 files changed, 457 insertions(+), 3 deletions(-) create mode 100644 modules/nf-core/cat/cat/environment.yml create mode 100644 modules/nf-core/cat/cat/main.nf create mode 100644 modules/nf-core/cat/cat/meta.yml create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test create mode 100644 modules/nf-core/cat/cat/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config create mode 100644 modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config create mode 100644 modules/nf-core/cat/cat/tests/tags.yml diff --git a/bin/check_fetchngs_samplesheet.py b/bin/check_fetchngs_samplesheet.py index 2e1edac9..41128254 100755 --- a/bin/check_fetchngs_samplesheet.py +++ b/bin/check_fetchngs_samplesheet.py @@ -35,6 +35,7 @@ def __init__( platform_col="instrument_platform", library_col="library_strategy", file1_col="fastq_1", + file2_col="fastq_2", **kwargs, ): """ @@ -49,6 +50,8 @@ def __init__( of the instrument (default "instrument_platform"). library_col (str): The name of the column that contains the strategy of the preparation of the library (default "library_strategy"). + file2_col (str): The name of the column that contains the second file path + for the paired-end read data (default "fastq_2"). """ super().__init__(**kwargs) self._accession_col = accession_col @@ -56,6 +59,7 @@ def __init__( self._platform_col = platform_col self._library_col = library_col self._file1_col = file1_col + self._file2_col = file2_col self._seen = set() self.modified = [] @@ -83,6 +87,8 @@ def _validate_file(self, row): if len(row[self._file1_col]) <= 0: raise AssertionError("Data file is required.") self._validate_data_format(row[self._file1_col]) + if row[self._file2_col]: + self._validate_data_format(row[self._file2_col]) def _validate_data_format(self, filename): """Assert that a given filename has one of the expected FASTQ extensions.""" @@ -165,7 +171,7 @@ def check_samplesheet(file_in, file_out): https://raw.githubusercontent.com/sanger-tol/blobtoolkit/main/assets/test/samplesheet.csv """ - required_columns = {"run_accession", "instrument_model", "instrument_platform", "library_strategy", "fastq_1"} + required_columns = {"run_accession", "instrument_model", "instrument_platform", "library_strategy", "fastq_1", "fastq_2"} # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. with file_in.open(newline="") as in_handle: reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) diff --git a/modules.json b/modules.json index 97f74e42..2efbb154 100644 --- a/modules.json +++ b/modules.json @@ -17,6 +17,11 @@ "installed_by": ["modules"], "patch": "modules/nf-core/busco/busco.diff" }, + "cat/cat": { + "branch": "master", + "git_sha": "d593e8f6b7d1bbbb2acf43a4b9efeeac8d6720f2", + "installed_by": ["modules"] + }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e", diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml new file mode 100644 index 00000000..17a04ef2 --- /dev/null +++ b/modules/nf-core/cat/cat/environment.yml @@ -0,0 +1,7 @@ +name: cat_cat +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/cat/main.nf b/modules/nf-core/cat/cat/main.nf new file mode 100644 index 00000000..970ab760 --- /dev/null +++ b/modules/nf-core/cat/cat/main.nf @@ -0,0 +1,70 @@ +process CAT_CAT { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' : + 'biocontainers/pigz:2.3.4' }" + + input: + tuple val(meta), path(files_in) + + output: + tuple val(meta), path("${prefix}"), emit: file_out + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def file_list = files_in.collect { it.toString() } + + // | input | output | command1 | command2 | + // |-----------|------------|----------|----------| + // | gzipped | gzipped | cat | | + // | ungzipped | ungzipped | cat | | + // | gzipped | ungzipped | zcat | | + // | ungzipped | gzipped | cat | pigz | + + // Use input file ending as default + prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + out_zip = prefix.endsWith('.gz') + in_zip = file_list[0].endsWith('.gz') + command1 = (in_zip && !out_zip) ? 'zcat' : 'cat' + command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : '' + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + $command1 \\ + $args \\ + ${file_list.join(' ')} \\ + $command2 \\ + > ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ + + stub: + def file_list = files_in.collect { it.toString() } + prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}" + if(file_list.contains(prefix.trim())) { + error "The name of the input file can't be the same as for the output prefix in the " + + "module CAT_CAT (currently `$prefix`). Please choose a different one." + } + """ + touch $prefix + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml new file mode 100644 index 00000000..00a8db0b --- /dev/null +++ b/modules/nf-core/cat/cat/meta.yml @@ -0,0 +1,36 @@ +name: cat_cat +description: A module for concatenation of gzipped or uncompressed files +keywords: + - concatenate + - gzip + - cat +tools: + - cat: + description: Just concatenation + documentation: https://man7.org/linux/man-pages/man1/cat.1.html + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - file_out: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" +authors: + - "@erikrikarddaniel" + - "@FriederikeHanssen" +maintainers: + - "@erikrikarddaniel" + - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/cat/tests/main.nf.test b/modules/nf-core/cat/cat/tests/main.nf.test new file mode 100644 index 00000000..ed5a4f12 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test @@ -0,0 +1,179 @@ +nextflow_process { + + name "Test Process CAT_CAT" + script "../main.nf" + process "CAT_CAT" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/cat" + + test("test_cat_name_conflict") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'genome', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") } + ) + } + } + + test("test_cat_unzipped_unzipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test_cat_zipped_zipped") { + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")} + ) + } + } + + test("test_cat_zipped_unzipped") { + config './nextflow_zipped_unzipped.config' + + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_cat_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")} + ) + } + } + + test("test_cat_one_file_unzipped_zipped") { + config './nextflow_unzipped_zipped.config' + when { + params { + outdir = "${outputDir}" + } + process { + """ + input[0] = + [ + [ id:'test', single_end:true ], + [ + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + ] + """ + } + } + then { + def lines = path(process.out.file_out.get(0).get(1)).linesGzip + assertAll( + { assert process.success }, + { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") }, + { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")} + ) + } + } +} + diff --git a/modules/nf-core/cat/cat/tests/main.nf.test.snap b/modules/nf-core/cat/cat/tests/main.nf.test.snap new file mode 100644 index 00000000..423571ba --- /dev/null +++ b/modules/nf-core/cat/cat/tests/main.nf.test.snap @@ -0,0 +1,121 @@ +{ + "test_cat_unzipped_zipped_size": { + "content": [ + 375 + ], + "timestamp": "2023-10-16T14:33:08.049445686" + }, + "test_cat_unzipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "test.fasta:md5,f44b33a0e441ad58b2d3700270e2dbe2" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:18.500464399" + }, + "test_cat_zipped_unzipped": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "1": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ], + "file_out": [ + [ + { + "id": "test", + "single_end": true + }, + "cat.txt:md5,c439d3b60e7bc03e8802a451a0d9a5d9" + ] + ], + "versions": [ + "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894" + ] + } + ], + "timestamp": "2023-10-16T14:32:49.642741302" + }, + "test_cat_zipped_zipped_lines": { + "content": [ + [ + "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab", + "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1", + "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1", + "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1", + "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1" + ] + ], + "timestamp": "2023-10-16T14:32:33.629048645" + }, + "test_cat_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:08.038830506" + }, + "test_cat_one_file_unzipped_zipped_lines": { + "content": [ + [ + ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome", + "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT", + "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG", + "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG", + "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT", + "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG" + ] + ], + "timestamp": "2023-10-16T14:33:21.39642399" + }, + "test_cat_zipped_zipped_size": { + "content": [ + 78 + ], + "timestamp": "2023-10-16T14:32:33.641869244" + }, + "test_cat_one_file_unzipped_zipped_size": { + "content": [ + 374 + ], + "timestamp": "2023-10-16T14:33:21.4094373" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config new file mode 100644 index 00000000..ec26b0fd --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_unzipped_zipped.config @@ -0,0 +1,6 @@ + +process { + withName: CAT_CAT { + ext.prefix = 'cat.txt.gz' + } +} diff --git a/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config new file mode 100644 index 00000000..fbc79783 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/nextflow_zipped_unzipped.config @@ -0,0 +1,8 @@ + +process { + + withName: CAT_CAT { + ext.prefix = 'cat.txt' + } + +} diff --git a/modules/nf-core/cat/cat/tests/tags.yml b/modules/nf-core/cat/cat/tests/tags.yml new file mode 100644 index 00000000..37b578f5 --- /dev/null +++ b/modules/nf-core/cat/cat/tests/tags.yml @@ -0,0 +1,2 @@ +cat/cat: + - modules/nf-core/cat/cat/** diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf index f8d515fd..c0f0ad34 100644 --- a/subworkflows/local/input_check.nf +++ b/subworkflows/local/input_check.nf @@ -2,6 +2,7 @@ // Check input samplesheet and get aligned read channels // +include { CAT_CAT } from '../../modules/nf-core/cat/cat/main' include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' include { FETCHNGSSAMPLESHEET_CHECK } from '../../modules/local/fetchngssamplesheet_check' include { BLOBTOOLKIT_CONFIG } from '../../modules/local/blobtoolkit/config' @@ -19,10 +20,23 @@ workflow INPUT_CHECK { FETCHNGSSAMPLESHEET_CHECK ( samplesheet ) .csv .splitCsv ( header:true, sep:',' ) - .map { create_data_channels_from_fetchngs(it) } - .set { aln } + .branch { row -> + paired: row.fastq_2 + [[id: row.run_accession, row:row], [row.fastq_1, row.fastq_2]] + not_paired: true + } + .set { reads_pairedness } ch_versions = ch_versions.mix ( FETCHNGSSAMPLESHEET_CHECK.out.versions.first() ) + CAT_CAT ( reads_pairedness.paired ) + ch_versions = ch_versions.mix ( CAT_CAT.out.versions.first() ) + + CAT_CAT.out.file_out + | map { meta, file -> meta.row + [fastq_1: file] } + | mix ( reads_pairedness.not_paired ) + | map { create_data_channels_from_fetchngs(it) } + | set { aln } + } else { SAMPLESHEET_CHECK ( samplesheet ) .csv