| 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": "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/fastk/fastk/environment.yml b/modules/nf-core/fastk/fastk/environment.yml new file mode 100644 index 00000000..14207ff6 --- /dev/null +++ b/modules/nf-core/fastk/fastk/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::false_flag # False flag to pass nf-core/lint diff --git a/modules/nf-core/fastk/fastk/fastk-fastk.diff b/modules/nf-core/fastk/fastk/fastk-fastk.diff index e019c85c..b39f0bb6 100644 --- a/modules/nf-core/fastk/fastk/fastk-fastk.diff +++ b/modules/nf-core/fastk/fastk/fastk-fastk.diff @@ -1,21 +1,12 @@ Changes in module 'nf-core/fastk/fastk' --- modules/nf-core/fastk/fastk/main.nf +++ modules/nf-core/fastk/fastk/main.nf -@@ -3,7 +3,7 @@ - label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. -- container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2' -+ container 'quay.io/sanger-tol/fastk:1.0.1-c1' - - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { -@@ -25,7 +25,7 @@ - script: +@@ -24,7 +24,7 @@ + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -+ def FASTK_VERSION = '427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. ++ def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ FastK \\ $args \\ diff --git a/modules/nf-core/fastk/fastk/main.nf b/modules/nf-core/fastk/fastk/main.nf index e953cd89..f51c9d90 100644 --- a/modules/nf-core/fastk/fastk/main.nf +++ b/modules/nf-core/fastk/fastk/main.nf @@ -3,12 +3,7 @@ process FASTK_FASTK { label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - container 'quay.io/sanger-tol/fastk:1.0.1-c1' - - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead." - } + container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2' input: tuple val(meta), path(reads) @@ -23,16 +18,54 @@ process FASTK_FASTK { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def FASTK_VERSION = '427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ FastK \\ $args \\ -T$task.cpus \\ + -M${task.memory.toGiga()} \\ -N${prefix}_fk \\ $reads + find . -name '*.ktab*' \\ + | xargs chmod a+r + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastk: $FASTK_VERSION + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + + def touch_ktab = args.contains('-t') ? "touch ${prefix}_fk.ktab .${prefix}_fk.ktab.1" : '' + def touch_prof = args.contains('-p') ? "touch ${prefix}_fk.prof .${prefix}_fk.pidx.1" : '' + """ + touch ${prefix}_fk.hist + $touch_ktab + $touch_prof + + echo \\ + "FastK \\ + $args \\ + -T$task.cpus \\ + -M${task.memory.toGiga()} \\ + -N${prefix}_fk \\ + $reads" + cat <<-END_VERSIONS > versions.yml "${task.process}": fastk: $FASTK_VERSION diff --git a/modules/nf-core/fastk/fastk/meta.yml b/modules/nf-core/fastk/fastk/meta.yml index 55fd1be7..4abc1033 100644 --- a/modules/nf-core/fastk/fastk/meta.yml +++ b/modules/nf-core/fastk/fastk/meta.yml @@ -8,45 +8,58 @@ tools: - "fastk": description: "A fast K-mer counter for high-fidelity shotgun datasets" homepage: "https://github.com/thegenemyers/FASTK" - tool_dev_url: "https://github.com/thegenemyers/FASTK" - - licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" - + licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" 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. - + - - 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 ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" - ktab: - type: file - description: A sorted table of all canonical k‑mers along with their counts. - pattern: "*.ktab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: A sorted table of all canonical k‑mers along with their counts. + pattern: "*.ktab" - prof: - type: file - description: A k‑mer count profile of each sequence in the input data set. - pattern: "*.prof" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: A k‑mer count profile of each sequence in the input data set. + pattern: "*.prof" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" +maintainers: + - "@mahesh-panchal" + - "@gallvp" diff --git a/modules/nf-core/fastk/fastk/tests/main.nf.test b/modules/nf-core/fastk/fastk/tests/main.nf.test new file mode 100644 index 00000000..856c36a8 --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/main.nf.test @@ -0,0 +1,110 @@ +nextflow_process { + + name "Test Process FASTK_FASTK" + script "../main.nf" + config './nextflow.config' + process "FASTK_FASTK" + + tag "modules" + tag "modules_nfcore" + tag "fastk" + tag "fastk/fastk" + + test("test_fastk_fastk_single_end") { + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_paired_end") { + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_single_end_stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_paired_end_stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fastk/fastk/tests/main.nf.test.snap b/modules/nf-core/fastk/fastk/tests/main.nf.test.snap new file mode 100644 index 00000000..1e3fc4da --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/main.nf.test.snap @@ -0,0 +1,346 @@ +{ + "test_fastk_fastk_single_end_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test_fk.hist:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + [ + ".test_fk.ktab.1:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_fk.ktab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + [ + ".test_fk.pidx.1:md5,d41d8cd98f00b204e9800998ecf8427e", + 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"test_fk.hist:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ktab": [ + [ + { + "id": "test", + "single_end": false + }, + [ + ".test_fk.ktab.1:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_fk.ktab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "prof": [ + [ + { + "id": "test", + "single_end": false + }, + [ + ".test_fk.pidx.1:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_fk.prof:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,c216a1608924d1662d2086e1de1d5abd" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-18T19:39:32.570957" + } +} \ No newline at end of file diff --git a/modules/nf-core/fastk/fastk/tests/nextflow.config b/modules/nf-core/fastk/fastk/tests/nextflow.config new file mode 100644 index 00000000..c89ce9d5 --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = '-t -p' +} diff --git a/modules/nf-core/fastk/fastk/tests/tags.yml b/modules/nf-core/fastk/fastk/tests/tags.yml new file mode 100644 index 00000000..82f9df82 --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/tags.yml @@ -0,0 +1,2 @@ +fastk/fastk: + - "modules/nf-core/fastk/fastk/**" diff --git a/modules/nf-core/gnu/sort/environment.yml b/modules/nf-core/gnu/sort/environment.yml new file mode 100644 index 00000000..babcfb55 --- /dev/null +++ b/modules/nf-core/gnu/sort/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::coreutils=9.3 diff --git a/modules/nf-core/gnu/sort/main.nf b/modules/nf-core/gnu/sort/main.nf index b0a57fbb..e1167666 100644 --- a/modules/nf-core/gnu/sort/main.nf +++ b/modules/nf-core/gnu/sort/main.nf @@ -1,11 +1,11 @@ process GNU_SORT { - tag "${meta.id}" + tag "$meta.id" label "process_low" - conda "bioconda::coreutils=8.25" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/coreutils:8.25--1' : - 'biocontainers/coreutils:8.25--1' }" + 'https://depot.galaxyproject.org/singularity/coreutils:9.3': + 'biocontainers/coreutils:9.3' }" input: tuple val(meta), path(input) @@ -22,7 +22,7 @@ process GNU_SORT { def prefix = task.ext.prefix ?: "${meta.id}" suffix = task.ext.suffix ?: "${input.extension}" output_file = "${prefix}.${suffix}" - def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = "9.3" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ sort ${args} ${input} > ${output_file} @@ -34,15 +34,14 @@ process GNU_SORT { """ stub: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" suffix = task.ext.suffix ?: "${input.extension}" output_file = "${prefix}.${suffix}" - def VERSION = "9.1" + def VERSION = "9.3" if ("$input" == "$output_file") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ - sort ${args} ${input} > ${output_file} + touch ${output_file} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml index e7fb0284..c555dbb5 100644 --- a/modules/nf-core/gnu/sort/meta.yml +++ b/modules/nf-core/gnu/sort/meta.yml @@ -1,4 +1,4 @@ -name: "GNU_SORT" +name: "gnu_sort" description: | Writes a sorted concatenation of file/s keywords: @@ -11,32 +11,30 @@ tools: homepage: "https://github.com/vgl-hub/gfastats" documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html" licence: ["GPL"] - + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Draft assembly file - pattern: "*.{txt,bed,interval,genome,bins}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Draft assembly file + pattern: "*.{txt,bed,interval,genome,bins}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: The sorted txt file generated by sort - pattern: "*.{txt,bed,interval,genome,bins}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" +maintainers: + - "@DLBPointon" diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test b/modules/nf-core/gnu/sort/tests/main.nf.test new file mode 100644 index 00000000..e4030187 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/main.nf.test @@ -0,0 +1,120 @@ +nextflow_process { + + name "Test Process GNU_SORT" + script "modules/nf-core/gnu/sort/main.nf" + process "GNU_SORT" + + tag "modules" + tag "modules_nfcore" + tag "gnu" + tag "gnu/sort" + + test("unsorted_genome_sort") { + config "./sort_simple_bed.config" + + when { + process { + """ + input[0] = [ + [id:'genome_test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['genome_file'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("genome_sort") + } + ) + } + + } + + test("unsorted_intervals_sort") { + config "./sort_simple_bed.config" + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['intervals'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("interval_sort") + } + ) + } + + } + + test("unsorted_csv_sort") { + config "./sort_complex.config" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.sorted[0][1]).name + ).match("csv_sort") + } + ) + } + + } + + test("unsorted_csv_sort_stub") { + config "./sort_complex.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [id:'test'], + file(params.test_data['generic']['unsorted_data']['unsorted_text']['numbers_csv'], + checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + +} diff --git a/modules/nf-core/gnu/sort/tests/main.nf.test.snap b/modules/nf-core/gnu/sort/tests/main.nf.test.snap new file mode 100644 index 00000000..63891bc4 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/main.nf.test.snap @@ -0,0 +1,164 @@ +{ + "unsorted_csv_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + ] + ], + "1": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,0b52d1b4c4a0c6e972c6f94aafd75a1d" + ] + ], + "versions": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:44.714632791" + }, + "interval_sort": { + "content": [ + "test.bed.sorted" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:37.962807086" + }, + "unsorted_csv_sort_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.csv.sorted:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:51.456258705" + }, + "csv_sort": { + "content": [ + "test.csv.sorted" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:44.725431761" + }, + "unsorted_genome_sort": { + "content": [ + { + "0": [ + [ + { + "id": "genome_test" + }, + "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + ] + ], + "1": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ], + "sorted": [ + [ + { + "id": "genome_test" + }, + "genome_test.bed.sorted:md5,fd97f7efafdbbfa71d9b560f10b4b048" + ] + ], + "versions": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:31.041778719" + }, + "genome_sort": { + "content": [ + "genome_test.bed.sorted" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:31.060201722" + }, + "unsorted_intervals_sort": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.sorted:md5,abbce903ef263d38b2f71856387799ab" + ] + ], + "1": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ], + "sorted": [ + [ + { + "id": "test" + }, + "test.bed.sorted:md5,abbce903ef263d38b2f71856387799ab" + ] + ], + "versions": [ + "versions.yml:md5,dd412503ec9dd665203e083ea44326cb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-14T11:13:37.951397547" + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_complex.config b/modules/nf-core/gnu/sort/tests/sort_complex.config new file mode 100644 index 00000000..103eaaf6 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_complex.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-t ';' -g -k 1,1 -k 2,2" } + ext.suffix = { "csv.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_bed.config b/modules/nf-core/gnu/sort/tests/sort_simple_bed.config new file mode 100644 index 00000000..d7d52e0f --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_simple_bed.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-k1,1 -k2,2n" } + ext.suffix = { "bed.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/sort_simple_genome.config b/modules/nf-core/gnu/sort/tests/sort_simple_genome.config new file mode 100644 index 00000000..4dcec385 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/sort_simple_genome.config @@ -0,0 +1,6 @@ +process { + withName: GNU_SORT { + ext.args = { "-k1,1 -k2,2n" } + ext.suffix = { "genome.sorted" } + } +} \ No newline at end of file diff --git a/modules/nf-core/gnu/sort/tests/tags.yml b/modules/nf-core/gnu/sort/tests/tags.yml new file mode 100644 index 00000000..ac40e376 --- /dev/null +++ b/modules/nf-core/gnu/sort/tests/tags.yml @@ -0,0 +1,2 @@ +gnu/sort: + - "modules/nf-core/gnu/sort/**" diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml new file mode 100644 index 00000000..c7794856 --- /dev/null +++ b/modules/nf-core/gunzip/environment.yml @@ -0,0 +1,7 @@ +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::grep=3.11 + - conda-forge::sed=4.8 + - conda-forge::tar=1.34 diff --git a/modules/nf-core/gunzip/main.nf b/modules/nf-core/gunzip/main.nf index e7189d2f..5e67e3b9 100644 --- a/modules/nf-core/gunzip/main.nf +++ b/modules/nf-core/gunzip/main.nf @@ -2,10 +2,10 @@ process GUNZIP { tag "$archive" label 'process_single' - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -18,13 +18,20 @@ process GUNZIP { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - gunzip = archive.toString() - '.gz' + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" """ - gunzip \\ - -f \\ + # Not calling gunzip itself because it creates files + # with the original group ownership rather than the + # default one for that user / the work directory + gzip \\ + -cd \\ $args \\ - $archive + $archive \\ + > $gunzip cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -33,7 +40,11 @@ process GUNZIP { """ stub: - gunzip = archive.toString() - '.gz' + def args = task.ext.args ?: '' + def extension = ( archive.toString() - '.gz' ).tokenize('.')[-1] + def name = archive.toString() - '.gz' - ".$extension" + def prefix = task.ext.prefix ?: name + gunzip = prefix + ".$extension" """ touch $gunzip cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index 4cdcdf4c..9066c035 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,26 +10,38 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" - "@jfy133" +maintainers: + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" + - "@gallvp" diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test new file mode 100644 index 00000000..776211ad --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test @@ -0,0 +1,121 @@ +nextflow_process { + + name "Test Process GUNZIP" + script "../main.nf" + process "GUNZIP" + tag "gunzip" + tag "modules_nfcore" + tag "modules" + + test("Should run without failures") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix") { + + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - stub") { + + options '-stub' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("Should run without failures - prefix - stub") { + + options '-stub' + config './nextflow.config' + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + ) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap new file mode 100644 index 00000000..069967e7 --- /dev/null +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "Should run without failures - prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:10.861293" + }, + "Should run without failures - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:35:05.857145" + }, + "Should run without failures": { + "content": [ + { + "0": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + [ + + ], + "test_1.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2023-10-17T15:35:37.690477896" + }, + "Should run without failures - prefix": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ], + "gunzip": [ + [ + { + "id": "test" + }, + "test.xyz.fastq:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,54376d32aca20e937a4ec26dac228e84" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-25T11:33:32.921739" + } +} \ No newline at end of file diff --git a/modules/nf-core/gunzip/tests/nextflow.config b/modules/nf-core/gunzip/tests/nextflow.config new file mode 100644 index 00000000..dec77642 --- /dev/null +++ b/modules/nf-core/gunzip/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GUNZIP { + ext.prefix = { "${meta.id}.xyz" } + } +} diff --git a/modules/nf-core/gunzip/tests/tags.yml b/modules/nf-core/gunzip/tests/tags.yml new file mode 100644 index 00000000..fd3f6915 --- /dev/null +++ b/modules/nf-core/gunzip/tests/tags.yml @@ -0,0 +1,2 @@ +gunzip: + - modules/nf-core/gunzip/** diff --git a/modules/nf-core/merquryfk/merquryfk/main.nf b/modules/nf-core/merquryfk/merquryfk/main.nf index 43bfe468..2a5ab221 100644 --- a/modules/nf-core/merquryfk/merquryfk/main.nf +++ b/modules/nf-core/merquryfk/merquryfk/main.nf @@ -3,48 +3,53 @@ process MERQURYFK_MERQURYFK { label 'process_medium' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - container 'quay.io/sanger-tol/fastk:1.0.1-c1' - - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - exit 1, "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead." - } + container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2' input: - tuple val(meta), path(fastk_hist), path(fastk_ktab), path(assembly), path(haplotigs) + tuple val(meta), path(fastk_hist),path(fastk_ktab),path(assembly),path(haplotigs) + path matktab //optional + path patktab //optional output: - tuple val(meta), path("${prefix}.completeness.stats") , emit: stats - tuple val(meta), path("${prefix}.*_only.bed") , emit: bed - tuple val(meta), path("${prefix}.*.qv") , emit: assembly_qv - tuple val(meta), path("${prefix}.*.spectra-cn.fl.png"), emit: spectra_cn_fl_png, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.fl.pdf"), emit: spectra_cn_fl_pdf, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.ln.png"), emit: spectra_cn_ln_png, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.ln.pdf"), emit: spectra_cn_ln_pdf, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.st.png"), emit: spectra_cn_st_png, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.st.pdf"), emit: spectra_cn_st_pdf, optional: true - tuple val(meta), path("${prefix}.qv") , emit: qv - tuple val(meta), path("${prefix}.spectra-asm.fl.png") , emit: spectra_asm_fl_png, optional: true - tuple val(meta), path("${prefix}.spectra-asm.fl.pdf") , emit: spectra_asm_fl_pdf, optional: true - tuple val(meta), path("${prefix}.spectra-asm.ln.png") , emit: spectra_asm_ln_png, optional: true - tuple val(meta), path("${prefix}.spectra-asm.ln.pdf") , emit: spectra_asm_ln_pdf, optional: true - tuple val(meta), path("${prefix}.spectra-asm.st.png") , emit: spectra_asm_st_png, optional: true - tuple val(meta), path("${prefix}.spectra-asm.st.pdf") , emit: spectra_asm_st_pdf, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.completeness.stats") , emit: stats + tuple val(meta), path("${prefix}.*_only.bed") , emit: bed + tuple val(meta), path("${prefix}.*.qv") , emit: assembly_qv + tuple val(meta), path("${prefix}.*.spectra-cn.fl.{png,pdf}") , emit: spectra_cn_fl, optional: true + tuple val(meta), path("${prefix}.*.spectra-cn.ln.{png,pdf}") , emit: spectra_cn_ln, optional: true + tuple val(meta), path("${prefix}.*.spectra-cn.st.{png,pdf}") , emit: spectra_cn_st, optional: true + tuple val(meta), path("${prefix}.qv") , emit: qv + tuple val(meta), path("${prefix}.spectra-asm.fl.{png,pdf}") , emit: spectra_asm_fl, optional: true + tuple val(meta), path("${prefix}.spectra-asm.ln.{png,pdf}") , emit: spectra_asm_ln, optional: true + tuple val(meta), path("${prefix}.spectra-asm.st.{png,pdf}") , emit: spectra_asm_st, optional: true + tuple val(meta), path("${prefix}.phased_block.bed") , emit: phased_block_bed, optional: true + tuple val(meta), path("${prefix}.phased_block.stats") , emit: phased_block_stats, optional: true + tuple val(meta), path("${prefix}.continuity.N.{pdf,png}") , emit: continuity_N, optional: true + tuple val(meta), path("${prefix}.block.N.{pdf,png}") , emit: block_N, optional: true + tuple val(meta), path("${prefix}.block.blob.{pdf,png}") , emit: block_blob, optional: true + tuple val(meta), path("${prefix}.hapmers.blob.{pdf,png}") , emit: hapmers_blob, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" - def FASTK_VERSION = '427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - def MERQURY_VERSION = 'd00d98157618f4e8d1a9190026b19b471055b22e' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : '' + def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : '' + def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def MERQURY_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ MerquryFK \\ $args \\ -T$task.cpus \\ ${fastk_ktab.find{ it.toString().endsWith(".ktab") }} \\ + ${mat_ktab} \\ + ${pat_ktab} \\ $assembly \\ $haplotigs \\ $prefix @@ -56,4 +61,20 @@ process MERQURYFK_MERQURYFK { r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' ) END_VERSIONS """ + stub: + prefix = task.ext.prefix ?: "${meta.id}" + def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.completeness.stats + touch ${prefix}.qv + touch ${prefix}._.qv + touch ${prefix}._only.bed + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastk: $FASTK_VERSION + merquryfk: $MERQURY_VERSION + r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff b/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff index c98c6057..b0ecbe5d 100644 --- a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff +++ b/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff @@ -1,23 +1,14 @@ Changes in module 'nf-core/merquryfk/merquryfk' --- modules/nf-core/merquryfk/merquryfk/main.nf +++ modules/nf-core/merquryfk/merquryfk/main.nf -@@ -3,7 +3,7 @@ - label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. -- container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2' -+ container 'quay.io/sanger-tol/fastk:1.0.1-c1' - - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { -@@ -38,8 +38,8 @@ - script: - def args = task.ext.args ?: '' +@@ -41,8 +41,8 @@ prefix = task.ext.prefix ?: "${meta.id}" + def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : '' + def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : '' - def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -+ def FASTK_VERSION = '427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -+ def MERQURY_VERSION = 'd00d98157618f4e8d1a9190026b19b471055b22e' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. ++ def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. ++ def MERQURY_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ MerquryFK \\ $args \\ diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml index ad89f8ba..82bfbec4 100644 --- a/modules/nf-core/merquryfk/merquryfk/meta.yml +++ b/modules/nf-core/merquryfk/merquryfk/meta.yml @@ -1,113 +1,217 @@ name: "merquryfk_merquryfk" description: FastK based version of Merqury keywords: - - sort + - Merqury + - reference-free + - assembly evaluation tools: - "merquryfk": description: "FastK based version of Merqury" homepage: "https://github.com/thegenemyers/MERQURY.FK" - tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" - - licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE" - + licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - assembly: - type: file - description: Genome (primary) assembly files (fasta format) - pattern: ".fasta" - - haplotigs: - type: file - description: Assembly haplotigs (fasta format) - pattern: ".fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" + - assembly: + type: file + description: Genome (primary) assembly files (fasta format) + pattern: ".fasta" + - haplotigs: + type: file + description: Assembly haplotigs (fasta format) + pattern: ".fasta" + - - matktab: + type: file + description: trio maternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" + - - patktab: + type: file + description: trio paternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.completeness.stats: + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - bed: - type: file - description: Assembly only kmer positions not supported by reads in bed format - pattern: "*_only.bed" - - spectra_cn_fl_png: - type: file - description: "Unstacked copy number spectra filled plot in PNG format" - pattern: "*.spectra-cn.fl.png" - - spectra_cn_ln_png: - type: file - description: "Unstacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.ln.png" - - spectra_cn_st_png: - type: file - description: "Stacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.st.png" - - spectra_asm_fl_png: - type: file - description: "Unstacked assembly spectra filled plot in PNG format" - pattern: "*.spectra-asm.fl.png" - - spectra_asm_ln_png: - type: file - description: "Unstacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.ln.png" - - spectra_asm_st_png: - type: file - description: "Stacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.st.png" - - spectra_cn_fl_pdf: - type: file - description: "Unstacked copy number spectra filled plot in PDF format" - pattern: "*.spectra-cn.fl.pdf" - - spectra_cn_ln_pdf: - type: file - description: "Unstacked copy number spectra line plot in PDF format" - pattern: "*.spectra-cn.ln.pdf" - - spectra_cn_st_pdf: - type: file - description: "Stacked copy number spectra line plot in PDF format" - pattern: "*.spectra-cn.st.pdf" - - spectra_asm_fl_pdf: - type: file - description: "Unstacked assembly spectra filled plot in PDF format" - pattern: "*.spectra-asm.fl.pdf" - - spectra_asm_ln_pdf: - type: file - description: "Unstacked assembly spectra line plot in PDF format" - pattern: "*.spectra-asm.ln.pdf" - - spectra_asm_st_pdf: - type: file - description: "Stacked assembly spectra line plot in PDF format" - pattern: "*.spectra-asm.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*_only.bed: + type: file + description: Assembly only kmer positions not supported by reads in bed format + pattern: "*_only.bed" - assembly_qv: - type: file - description: "error and qv table for each scaffold of the assembly" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "error and qv table for each scaffold of the assembly" + pattern: "*.qv" + - spectra_cn_fl: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.fl.{png,pdf}: + type: file + description: "Unstacked copy number spectra filled plot in PNG or PDF format" + pattern: "*.spectra-cn.fl.{png,pdf}" + - spectra_cn_ln: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.ln.{png,pdf}: + type: file + description: "Unstacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.ln.{png,pdf}" + - spectra_cn_st: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.st.{png,pdf}: + type: file + description: "Stacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.st.{png,pdf}" - qv: - type: file - description: "error and qv of each assembly as a whole" - pattern: "*.qv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "error and qv of each assembly as a whole" + pattern: "*.qv" + - spectra_asm_fl: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.fl.{png,pdf}: + type: file + description: "Unstacked assembly spectra filled plot in PNG or PDF format" + pattern: "*.spectra-asm.fl.{png,pdf}" + - spectra_asm_ln: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.ln.{png,pdf}: + type: file + description: "Unstacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.ln.{png,pdf}" + - spectra_asm_st: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.st.{png,pdf}: + type: file + description: "Stacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.st.{png,pdf}" + - phased_block_bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.bed: + type: file + description: Assembly kmer positions seperated by block in bed format + pattern: "*.phased.block.bed" + - phased_block_stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.stats: + type: file + description: phased assembly statistics file + pattern: "*.phased.block.stats" + - continuity_N: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.continuity.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity plot in PNG or PDF format" + pattern: "*.continuity.N.{png,pdf}" + - block_N: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity by block plot in PNG or PDF format" + pattern: "*.block.N.{png,pdf}" + - block_blob: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.blob.{pdf,png}: + type: file + description: "Stacked assembly block plot in PNG or PDF format" + pattern: "*.block.blob.{png,pdf}" + - hapmers_blob: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hapmers.blob.{pdf,png}: + type: file + description: "Stacked assembly hapmers block plot in PNG or PDF format" + pattern: "*.hapmers.blob.{png,pdf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" + - "@yumisims" +maintainers: + - "@mahesh-panchal" + - "@yumisims" diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test new file mode 100644 index 00000000..c46843c6 --- /dev/null +++ b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test @@ -0,0 +1,170 @@ +nextflow_process { + + name "Test Process MERQURYFK" + script "../main.nf" + process "MERQURYFK_MERQURYFK" + + tag "modules" + tag "modules_nfcore" + tag "merquryfk" + tag "merquryfk/merquryfk" + tag "fastk" + tag "fastk/fastk" + + setup { + run("FASTK_FASTK") { + script "../../../fastk/fastk" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + run("FASTK_FASTK", alias: "FASTK_MAT") { + script "../../../fastk/fastk" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + ] + """ + } + } + + run("FASTK_FASTK", alias: "FASTK_PAT") { + script "../../../fastk/fastk" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + ] + """ + } + } + } + + test("homo_sapiens - Illumina - png") { + config "./nextflow.png.config" + when { + process { + """ + assembly = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + + haplotigs = [ + [ id:'test', single_end:true ], [] + ] + input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - Illumina - pdf") { + config "./nextflow.pdf.config" + when { + process { + """ + assembly = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + + haplotigs = [ + [ id:'test', single_end:true ], [] + ] + input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - Illumina - trio") { + config "./nextflow.trio.config" + when { + process { + """ + assembly = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + + haplotigs = [ + [ id:'test', single_end:true ], [] + ] + input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) + input[1] = FASTK_MAT.out.ktab + input[2] = FASTK_PAT.out.ktab + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - Illumina - stub") { + options "-stub" + config "./nextflow.pdf.config" + when { + process { + """ + assembly = [ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + + haplotigs = [ + [ id:'test', single_end:true ], [] + ] + input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + + +} \ No newline at end of file diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap new file mode 100644 index 00000000..f7ce47f0 --- /dev/null +++ b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap @@ -0,0 +1,454 @@ +{ + "homo_sapiens - 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"modules/nf-core/merquryfk/merquryfk/**" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 00000000..6f5b867b --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387be..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,16 +1,18 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,14 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' 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}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ + $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -41,8 +51,8 @@ process MULTIQC { stub: """ - touch multiqc_data - touch multiqc_plots + mkdir multiqc_data + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee5..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,6 +1,6 @@ -# 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 +name: multiqc +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -13,44 +13,66 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@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..33316a7d --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,92 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + config "./nextflow.config" + + test("sarscov2 single-end [fastqc]") { + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + 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("multiqc_versions_single") } + ) + } + + } + + test("sarscov2 single-end [fastqc] [config]") { + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_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] = [] + input[4] = [] + input[5] = [] + """ + } + } + + 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("multiqc_versions_config") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + input[5] = [] + """ + } + } + + 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("multiqc_stub") } + ) + } + + } +} 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..2fcbb5ff --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "multiqc_versions_single": { + "content": [ + [ + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:51:46.317523" + }, + "multiqc_stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:52:20.680978" + }, + "multiqc_versions_config": { + "content": [ + [ + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-02T17:52:09.185842" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} 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/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml new file mode 100644 index 00000000..02cda6e6 --- /dev/null +++ b/modules/nf-core/samtools/view/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + # renovate: datasource=conda depName=bioconda/htslib + - bioconda::htslib=1.21 + # renovate: datasource=conda depName=bioconda/samtools + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index b87369e5..a6941e63 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -2,24 +2,26 @@ process SAMTOOLS_VIEW { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9edc2564215d5cd137a8b25ca8a311600987186d406b092022444adf3c4447f7/data' : + 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' }" input: tuple val(meta), path(input), path(index) - path fasta + tuple val(meta2), path(fasta) path qname output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.sam"), emit: sam, optional: true - tuple val(meta), path("*.bai"), emit: bai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - path "versions.yml", emit: versions + tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true + tuple val(meta), path("${prefix}.cram"), emit: cram, optional: true + tuple val(meta), path("${prefix}.sam"), emit: sam, optional: true + tuple val(meta), path("${prefix}.${file_type}.bai"), emit: bai, optional: true + tuple val(meta), path("${prefix}.${file_type}.csi"), emit: csi, optional: true + tuple val(meta), path("${prefix}.${file_type}.crai"), emit: crai, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}"), emit: unselected, optional: true + tuple val(meta), path("${prefix}.unselected.${file_type}.{bai,csi,crsi}"), emit: unselected_index, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -27,13 +29,13 @@ process SAMTOOLS_VIEW { script: def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" - def readnames = qname ? "--qname-file ${qname}": "" - def file_type = args.contains("--output-fmt sam") ? "sam" : - args.contains("--output-fmt bam") ? "bam" : - args.contains("--output-fmt cram") ? "cram" : - input.getExtension() + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + readnames = qname ? "--qname-file ${qname} --output-unselected ${prefix}.unselected.${file_type}": "" if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" """ samtools \\ @@ -53,10 +55,19 @@ process SAMTOOLS_VIEW { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + file_type = args.contains("--output-fmt sam") ? "sam" : + args.contains("--output-fmt bam") ? "bam" : + args.contains("--output-fmt cram") ? "cram" : + input.getExtension() + if ("$input" == "${prefix}.${file_type}") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + + index = args.contains("--write-index") ? "touch ${prefix}.${file_type}.csi" : "" + """ - touch ${prefix}.bam - touch ${prefix}.cram + touch ${prefix}.${file_type} + ${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 76916033..caa7b015 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -15,65 +15,127 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: optional file - description: BAM.BAI/BAM.CSI/CRAM.CRAI file - pattern: "*.{.bai,.csi,.crai}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - pattern: "*.{fasta,fa}" - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) + pattern: "*.{.bai,.csi,.crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: optional filtered/converted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: optional filtered/converted BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/converted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: optional filtered/converted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/converted SAM file - pattern: "*.{sam}" - # bai, csi, and crai are created with `--write-index` + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: optional filtered/converted SAM file + pattern: "*.{sam}" - bai: - type: file - description: optional BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.bai: + type: file + description: optional BAM file index + pattern: "*.{bai}" - csi: - type: file - description: optional tabix BAM file index - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.csi: + type: file + description: optional tabix BAM file index + pattern: "*.{csi}" - crai: - type: file - description: optional CRAM file index - pattern: "*.{crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.crai: + type: file + description: optional CRAM file index + pattern: "*.{crai}" + - unselected: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" + - unselected_index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}.{bai,csi,crsi}: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" - "@FriederikeHanssen" - "@priyanka-surana" +maintainers: + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" + - "@priyanka-surana" diff --git a/modules/nf-core/samtools/view/tests/bam.config b/modules/nf-core/samtools/view/tests/bam.config new file mode 100644 index 00000000..c10d1081 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/bam.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-fmt bam" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/bam_index.config b/modules/nf-core/samtools/view/tests/bam_index.config new file mode 100644 index 00000000..771ae033 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/bam_index.config @@ -0,0 +1,3 @@ +process { + ext.args = "--output-fmt bam --write-index" +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/main.nf.test b/modules/nf-core/samtools/view/tests/main.nf.test new file mode 100644 index 00000000..37b81a91 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/main.nf.test @@ -0,0 +1,214 @@ +nextflow_process { + + name "Test Process SAMTOOLS_VIEW" + script "../main.nf" + process "SAMTOOLS_VIEW" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/view" + + test("bam") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_bam") }, + { assert snapshot(process.out.bai).match("bam_bai") }, + { assert snapshot(process.out.crai).match("bam_crai") }, + { assert snapshot(process.out.cram).match("bam_cram") }, + { assert snapshot(process.out.csi).match("bam_csi") }, + { assert snapshot(process.out.sam).match("bam_sam") }, + { assert snapshot(process.out.versions).match("bam_versions") } + ) + } + } + + test("cram") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.cram[0][1]).name).match("cram_cram") }, + { assert snapshot(process.out.bai).match("cram_bai") }, + { assert snapshot(process.out.bam).match("cram_bam") }, + { assert snapshot(process.out.crai).match("cram_crai") }, + { assert snapshot(process.out.csi).match("cram_csi") }, + { assert snapshot(process.out.sam).match("cram_sam") }, + { assert snapshot(process.out.versions).match("cram_versions") } + ) + } + } + + test("cram_to_bam") { + + config "./bam.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_bam") }, + { assert snapshot(process.out.bai).match("cram_to_bam_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_cram") }, + { assert snapshot(process.out.csi).match("cram_to_bam_csi") }, + { assert snapshot(process.out.sam).match("cram_to_bam_sam") }, + { assert snapshot(process.out.versions).match("cram_to_bam_versions") } + ) + } + } + + test("cram_to_bam_index") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_csi") }, + { assert snapshot(process.out.bai).match("cram_to_bam_index_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_index_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_index_cram") }, + { assert snapshot(process.out.sam).match("cram_to_bam_index_sam") }, + { assert snapshot(process.out.versions).match("cram_to_bam_index_versions") } + ) + } + } + + test("cram_to_bam_index_qname") { + + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = Channel.of("testN:2817", "testN:2814").collectFile(name: "readnames.list", newLine: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("cram_to_bam_index_qname_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("cram_to_bam_index_qname_csi") }, + { assert snapshot(process.out.bai).match("cram_to_bam_index_qname_bai") }, + { assert snapshot(process.out.crai).match("cram_to_bam_index_qname_crai") }, + { assert snapshot(process.out.cram).match("cram_to_bam_index_qname_cram") }, + { assert snapshot(process.out.sam).match("cram_to_bam_index_qname_sam") }, + { assert snapshot(file(process.out.unselected[0][1]).name).match("cram_to_bam_index_qname_unselected") }, + { assert snapshot(file(process.out.unselected_index[0][1]).name).match("cram_to_bam_index_qname_unselected_csi") }, + { assert snapshot(process.out.versions).match("cram_to_bam_index_qname_versions") } + ) + } + } + + test("bam_stub") { + + options "-stub" + config "./bam_index.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), + [] + ]) + input[1] = [[],[]] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(file(process.out.bam[0][1]).name).match("bam_stub_bam") }, + { assert snapshot(file(process.out.csi[0][1]).name).match("bam_stub_csi") }, + { assert snapshot(process.out.bai).match("bam_stub_bai") }, + { assert snapshot(process.out.crai).match("bam_stub_crai") }, + { assert snapshot(process.out.cram).match("bam_stub_cram") }, + { assert snapshot(process.out.sam).match("bam_stub_sam") }, + { assert snapshot(process.out.versions).match("bam_stub_versions") } + ) + } + } +} diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap new file mode 100644 index 00000000..63849b03 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -0,0 +1,528 @@ +{ + "bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.256068" + }, + "cram_to_bam_index_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.958617" + }, + "bam_stub_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.065301" + }, + "bam_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.258578" + }, + "bam_stub_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.071284" + }, + "bam_stub_versions": { + "content": [ + [ + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:26:24.461775464" + }, + "cram_to_bam_index_cram": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.972288" + }, + "cram_to_bam_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.999247" + }, + "cram_to_bam_index_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.976457" + }, + "cram_crai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.497581" + }, + "cram_csi": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.50038" + }, + "cram_to_bam_cram": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.992239" + }, + "cram_to_bam_index_qname_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.325496" + }, + "bam_stub_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.079529" + }, + "cram_cram": { + "content": [ + "test.cram" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.490286" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, + "bam_csi": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.262882" + }, + "cram_to_bam_crai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.989247" + }, + "cram_to_bam_index_crai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.967681" + }, + "cram_to_bam_index_qname_versions": { + "content": [ + [ + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:25:51.953436682" + }, + "cram_to_bam_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.982361" + }, + "cram_to_bam_index_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.95456" + }, + "cram_to_bam_index_versions": { + "content": [ + [ + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:25:14.475388399" + }, + "cram_to_bam_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:04.98601" + }, + "cram_to_bam_versions": { + "content": [ + [ + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:24:49.673441798" + }, + "cram_bam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.495512" + }, + "bam_stub_cram": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.076908" + }, + "cram_to_bam_index_qname_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, + "cram_to_bam_index_qname_crai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.330789" + }, + "cram_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:56.493129" + }, + "bam_stub_crai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.074313" + }, + "cram_to_bam_index_qname_bam": { + "content": [ + "test.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, + "bam_versions": { + "content": [ + [ + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" + ] + ], + "meta": { + "nf-test": "0.9.0", + 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"meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:24:12.95416913" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "bam_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:37:51.264651" + }, + "cram_to_bam_index_bai": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:12.962863" + }, + "cram_to_bam_index_qname_sam": { + "content": [ + [ + + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.337634" + }, + "bam_stub_csi": { + "content": [ + "test.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:32.068596" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/view/tests/tags.yml b/modules/nf-core/samtools/view/tests/tags.yml new file mode 100644 index 00000000..4fdf1dd1 --- /dev/null +++ b/modules/nf-core/samtools/view/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/view: + - "modules/nf-core/samtools/view/**" diff --git a/subworkflows/local/contact_maps.nf b/subworkflows/local/contact_maps.nf index ca784baf..eb686863 100644 --- a/subworkflows/local/contact_maps.nf +++ b/subworkflows/local/contact_maps.nf @@ -32,12 +32,7 @@ workflow CONTACT_MAPS { // CRAM to BAM - genome - | map { meta, fasta -> fasta } - | first - | set { ch_fasta } - - SAMTOOLS_VIEW ( reads, ch_fasta, [] ) + SAMTOOLS_VIEW ( reads, genome.first(), [] ) ch_versions = ch_versions.mix ( SAMTOOLS_VIEW.out.versions.first() ) @@ -71,7 +66,7 @@ workflow CONTACT_MAPS { GET_CHROMLIST.out.list | map { meta, list -> list } | first - | set { ch_chromsizes } + | set { ch_chromsizes } COOLER_CLOAD ( ch_cooler, ch_chromsizes ) ch_versions = ch_versions.mix ( COOLER_CLOAD.out.versions.first() ) @@ -89,7 +84,7 @@ workflow CONTACT_MAPS { // Create the `.genome` file COOLER_CLOAD.out.cool | map { meta, cool, bin -> [ meta, cool, [] ] } - | set { ch_dump } + | set { ch_dump } COOLER_DUMP ( ch_dump ) ch_versions = ch_versions.mix ( COOLER_DUMP.out.versions.first() ) diff --git a/subworkflows/local/genome_statistics.nf b/subworkflows/local/genome_statistics.nf index 73a7e2ba..e8807f96 100644 --- a/subworkflows/local/genome_statistics.nf +++ b/subworkflows/local/genome_statistics.nf @@ -5,7 +5,7 @@ include { NCBIDATASETS_SUMMARYGENOME as SUMMARYGENOME } from '../../modules/local/ncbidatasets/summarygenome' include { NCBIDATASETS_SUMMARYGENOME as SUMMARYSEQUENCE } from '../../modules/local/ncbidatasets/summarygenome' include { NCBI_GET_ODB } from '../../modules/local/ncbidatasets/get_odb' -include { BUSCO } from '../../modules/nf-core/busco/main' +include { BUSCO_BUSCO as BUSCO } from '../../modules/nf-core/busco/busco/main' include { RESTRUCTUREBUSCODIR } from '../../modules/local/restructurebuscodir' include { FASTK_FASTK } from '../../modules/nf-core/fastk/fastk/main' include { MERQURYFK_MERQURYFK } from '../../modules/nf-core/merquryfk/merquryfk/main' @@ -46,7 +46,7 @@ workflow GENOME_STATISTICS { | splitCsv() | map { row -> row[1] } | set { ch_lineage } - + BUSCO ( genome, "genome", ch_lineage, lineage_db.ifEmpty([]), [] ) ch_versions = ch_versions.mix ( BUSCO.out.versions.first() ) @@ -87,7 +87,7 @@ workflow GENOME_STATISTICS { FASTK_FASTK.out.hist | join ( FASTK_FASTK.out.ktab ) | set { ch_combo } - + ch_pacbio.dir | map { meta, dir -> [ meta, @@ -95,7 +95,7 @@ workflow GENOME_STATISTICS { dir.listFiles().findAll { it.toString().contains(".ktab") } .collect(), ] } | set { ch_grab } - + ch_combo | mix ( ch_grab ) | combine ( genome ) @@ -104,7 +104,7 @@ workflow GENOME_STATISTICS { // MerquryFK - MERQURYFK_MERQURYFK ( ch_merq ) + MERQURYFK_MERQURYFK ( ch_merq, [], [] ) ch_versions = ch_versions.mix ( MERQURYFK_MERQURYFK.out.versions.first() ) @@ -112,11 +112,11 @@ workflow GENOME_STATISTICS { SUMMARYGENOME.out.summary | join ( SUMMARYSEQUENCE.out.summary ) | set { ch_summary } - + BUSCO.out.short_summaries_json | ifEmpty ( [ [], [] ] ) | set { ch_busco } - + MERQURYFK_MERQURYFK.out.qv | join ( MERQURYFK_MERQURYFK.out.stats ) | map { meta, qv, comp -> [ meta + [ id: "merq" ], qv, comp ] } diff --git a/workflows/genomenote.nf b/workflows/genomenote.nf index c46e7a52..8964f117 100644 --- a/workflows/genomenote.nf +++ b/workflows/genomenote.nf @@ -160,7 +160,9 @@ workflow GENOMENOTE { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) multiqc_report = MULTIQC.out.report.toList()