diff --git a/modules/nf-core/trycycler/cluster/environment.yml b/modules/nf-core/trycycler/cluster/environment.yml new file mode 100644 index 00000000000..52adae7015b --- /dev/null +++ b/modules/nf-core/trycycler/cluster/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "trycycler_cluster" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::trycycler=0.5.3" diff --git a/modules/nf-core/trycycler/cluster/main.nf b/modules/nf-core/trycycler/cluster/main.nf new file mode 100644 index 00000000000..045a7ba908f --- /dev/null +++ b/modules/nf-core/trycycler/cluster/main.nf @@ -0,0 +1,56 @@ +process TRYCYCLER_CLUSTER { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/trycycler:0.5.3--pyhdfd78af_0': + 'biocontainers/trycycler:0.5.3--pyhdfd78af_0' }" + + input: + tuple val(meta), path(contigs), path(reads) + + output: + tuple val(meta), path("*") , emit: cluster_dir + 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 prefix = task.ext.prefix ?: "${meta.id}" + + """ + trycycler \\ + cluster \\ + $args \\ + --assemblies ${contigs} \\ + --reads ${reads} \\ + --threads $task.cpus \\ + --out_dir ${prefix} + + gzip $args2 ${prefix}/cluster_*/*/*.fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trycycler: \$(trycycler --version | sed 's/Trycycler v//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p ${prefix}/cluster_001/1_contigs + echo "" | gzip > ${prefix}/cluster_001/1_contigs/A_contig_2a.fasta.gz + touch ${prefix}/contigs.newick + touch ${prefix}/contigs.phylip + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trycycler: \$(trycycler --version | sed 's/Trycycler v//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/trycycler/cluster/meta.yml b/modules/nf-core/trycycler/cluster/meta.yml new file mode 100644 index 00000000000..a17357b9341 --- /dev/null +++ b/modules/nf-core/trycycler/cluster/meta.yml @@ -0,0 +1,55 @@ +name: "trycycler_cluster" +description: Cluster contigs from multiple assemblies by similarity +keywords: + - cluster + - alignment + - fastq + - fasta + - genomics +tools: + - "trycycler": + description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + homepage: https://github.com/rrwick/Trycycler + documentation: https://github.com/rrwick/Trycycler/wiki + doi: 10.1186/s13059-021-02483-z + licence: ["GPL v3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed + + - assemblies: + type: file + description: Input assemblies whose contigs will be clustered + + - out_dir: + type: directory + description: Output directory for clustering results + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - cluster_dir: + type: directory + description: Output directory containing clustering results + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@watsonar" +maintainers: + - "@watsonar" diff --git a/modules/nf-core/trycycler/cluster/tests/main.nf.test b/modules/nf-core/trycycler/cluster/tests/main.nf.test new file mode 100644 index 00000000000..e07230afedb --- /dev/null +++ b/modules/nf-core/trycycler/cluster/tests/main.nf.test @@ -0,0 +1,77 @@ +nextflow_process { + + name "Test Process TRYCYCLER_CLUSTER" + script "../main.nf" + process "TRYCYCLER_CLUSTER" + config './nextflow.config' + + tag "modules" + tag "modules_nfcore" + tag "trycycler" + tag "trycycler/cluster" + + test("custom test data") { + + when { + process { + """ + def contigs1 = file("contigs1.fasta") + contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n' + + def contigs2 = file("contigs2.fasta") + contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n' + + def reads = file("reads.fastq") + reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n@NC-000913.3_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n' + + input[0] = [ + [ id:'test' ], // meta map + [ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs + file('reads.fastq', checkIfExists: true) // reads + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("custom test data - stub") { + + when { + process { + options "-stub-run" + """ + def contigs1 = file("contigs1.fasta") + contigs1.text = '>contig_1a\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGATCACGACTACAGCACAGCACTACAGCATCAGCACAGCAGTCAGCGA\\n>contig_2a\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTATCGCAGCTACGATCAGCATCGATCTAGCAGAGCCTTCTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n' + + def contigs2 = file("contigs2.fasta") + contigs2.text = '>contig_1b\\nATCCCCTTGGACTCCTAGCTAGGCTCTAGAGCCTTCTCTCGACTACCCAGCTAGCAGCTACGATCACGTCTACAGCACAGCACTACAGCATCAGCACAGCAGTA\\n>contig_2b\\nGCTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGCAGCTACGATCAGCATCCATCTAGCAGAGCCAACTGGTAACGCGACTCAGTCTCTACAGCACGGTAACCAGCACTACAGGGGTTAAGCCCATCA\\n' + + def reads = file("reads.fastq") + reads.text = '@NC-000913.3_646515_unaligned_0_F_0_1238_0\\nCTCTAGAGCCTTCTCTCGACTACGAGCTAGCAGCTACGA\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n@NC-000913.3_646518_unaligned_0_F_0_1238_0\\nTAGGCTCTAACGCGCCATCAGCCGCTCAGCTACGACTAGCGC\\n+\\nIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\\n' + + input[0] = [ + [ id:'test' ], // meta map + [ file('contigs1.fasta', checkIfExists: true), file('contigs2.fasta', checkIfExists: true) ], // contigs + file('reads.fastq', checkIfExists: true) // reads + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } +} diff --git a/modules/nf-core/trycycler/cluster/tests/main.nf.test.snap b/modules/nf-core/trycycler/cluster/tests/main.nf.test.snap new file mode 100644 index 00000000000..7ddc55a7ab0 --- /dev/null +++ b/modules/nf-core/trycycler/cluster/tests/main.nf.test.snap @@ -0,0 +1,142 @@ +{ + "custom test data - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + [ + [ + "A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + ] + ], + "1": [ + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ], + "cluster_dir": [ + [ + { + "id": "test" + }, + [ + [ + [ + [ + "A_contig_2a.fasta.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "contigs.newick:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + ] + ], + "versions": [ + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-22T14:59:36.502272455" + }, + "custom test data": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + [ + [ + [ + "A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5" + ] + ], + [ + [ + "B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e" + ] + ], + [ + [ + "A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798" + ] + ], + [ + [ + "B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71" + ] + ], + "contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab", + "contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1" + ], + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + ] + ], + "1": [ + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ], + "cluster_dir": [ + [ + { + "id": "test" + }, + [ + [ + [ + [ + "A_contig_2a.fasta.gz:md5,2c579f9cc210a544772daa7f4a16d0d5" + ] + ], + [ + [ + "B_contig_2b.fasta.gz:md5,4b4819e6b8f996d387216450b314798e" + ] + ], + [ + [ + "A_contig_1a.fasta.gz:md5,6d49552461c330871cecac80635c1798" + ] + ], + [ + [ + "B_contig_1b.fasta.gz:md5,f012c88fa34c176735737485eb730d71" + ] + ], + "contigs.newick:md5,1793ccb2bff4a79525a1ce60fb90f8ab", + "contigs.phylip:md5,984639efc8ae4b4cbe6e53bdb0b8b8c1" + ], + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + ] + ], + "versions": [ + "versions.yml:md5,616584ce01fb659316a99b1329e047aa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-22T14:59:28.088111496" + } +} \ No newline at end of file diff --git a/modules/nf-core/trycycler/cluster/tests/nextflow.config b/modules/nf-core/trycycler/cluster/tests/nextflow.config new file mode 100644 index 00000000000..b0d8c05e32d --- /dev/null +++ b/modules/nf-core/trycycler/cluster/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: TRYCYCLER_CLUSTER { + ext.args = '--min_contig_len 0 --min_contig_depth 0' + } +} diff --git a/modules/nf-core/trycycler/cluster/tests/tags.yml b/modules/nf-core/trycycler/cluster/tests/tags.yml new file mode 100644 index 00000000000..7a36cbbbb07 --- /dev/null +++ b/modules/nf-core/trycycler/cluster/tests/tags.yml @@ -0,0 +1,2 @@ +trycycler/cluster: + - "modules/nf-core/trycycler/cluster/**" diff --git a/modules/nf-core/trycycler/subsample/environment.yml b/modules/nf-core/trycycler/subsample/environment.yml new file mode 100644 index 00000000000..0713e720deb --- /dev/null +++ b/modules/nf-core/trycycler/subsample/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +name: "trycycler_subsample" +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - "bioconda::trycycler=0.5.3" diff --git a/modules/nf-core/trycycler/subsample/main.nf b/modules/nf-core/trycycler/subsample/main.nf new file mode 100644 index 00000000000..9201f4ff007 --- /dev/null +++ b/modules/nf-core/trycycler/subsample/main.nf @@ -0,0 +1,60 @@ +process TRYCYCLER_SUBSAMPLE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/trycycler:0.5.3--pyhdfd78af_0': + 'biocontainers/trycycler:0.5.3--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*/*.fastq.gz") , emit: subreads + 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 prefix = task.ext.prefix ?: "${meta.id}" + + """ + trycycler \\ + subsample \\ + $args \\ + --reads ${reads} \\ + --threads $task.cpus \\ + --out_dir ${prefix} + + gzip $args2 ${prefix}/*.fastq + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trycycler: \$(trycycler --version | sed 's/Trycycler v//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + // Pull out the count integer from the args string, if provided + // Otherwise use default value of 12 + def matches = (args =~ /--count\s+(\d+)/) + def count = matches ? matches[0][1] as Integer : 12 + """ + for n in \$(seq $count); do + printf -v i "%02d" \$n + mkdir -p ${prefix} + echo "" | gzip > ${prefix}/sample_\${i}.fastq.gz + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trycycler: \$(trycycler --version | sed 's/Trycycler v//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/trycycler/subsample/meta.yml b/modules/nf-core/trycycler/subsample/meta.yml new file mode 100644 index 00000000000..38c7f9b232f --- /dev/null +++ b/modules/nf-core/trycycler/subsample/meta.yml @@ -0,0 +1,50 @@ +name: trycycler_subsample +description: Subsample a long-read sequencing fastq file for multiple assemblies +keywords: + - subsample + - fastq + - genomics +tools: + - "trycycler": + description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + homepage: https://github.com/rrwick/Trycycler + documentation: https://github.com/rrwick/Trycycler/wiki + doi: 10.1186/s13059-021-02483-z + licence: ["GPL v3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed + + - out_dir: + type: directory + description: Output directory for subsampled read sets + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - subreads: + type: file + description: Subsampled read sets + pattern: "*.{fastq.gz}" + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@watsonar" +maintainers: + - "@watsonar" diff --git a/modules/nf-core/trycycler/subsample/tests/config_1.config b/modules/nf-core/trycycler/subsample/tests/config_1.config new file mode 100644 index 00000000000..7fd57d6d6cb --- /dev/null +++ b/modules/nf-core/trycycler/subsample/tests/config_1.config @@ -0,0 +1,5 @@ +process { + withName: TRYCYCLER_SUBSAMPLE { + ext.args = '--count 10' + } +} diff --git a/modules/nf-core/trycycler/subsample/tests/config_2.config b/modules/nf-core/trycycler/subsample/tests/config_2.config new file mode 100644 index 00000000000..2dc2b220212 --- /dev/null +++ b/modules/nf-core/trycycler/subsample/tests/config_2.config @@ -0,0 +1,5 @@ +process { + withName: TRYCYCLER_SUBSAMPLE { + ext.args = '' + } +} diff --git a/modules/nf-core/trycycler/subsample/tests/main.nf.test b/modules/nf-core/trycycler/subsample/tests/main.nf.test new file mode 100644 index 00000000000..10b20f91b25 --- /dev/null +++ b/modules/nf-core/trycycler/subsample/tests/main.nf.test @@ -0,0 +1,82 @@ +nextflow_process { + + name "Test Process TRYCYCLER_SUBSAMPLE" + script "../main.nf" + process "TRYCYCLER_SUBSAMPLE" + + tag "modules" + tag "modules_nfcore" + tag "trycycler" + tag "trycycler/subsample" + + test("candidatus_portiera_aleyrodidarum - default") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("candidatus_portiera_aleyrodidarum - stub, ext args") { + + when { + config "./config_1.config" + process { + options "-stub-run" + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("candidatus_portiera_aleyrodidarum - stub, no ext args") { + + when { + config "./config_2.config" + process { + options "-stub-run" + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/nanopore/fastq/test.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/trycycler/subsample/tests/main.nf.test.snap b/modules/nf-core/trycycler/subsample/tests/main.nf.test.snap new file mode 100644 index 00000000000..2845904ea97 --- /dev/null +++ b/modules/nf-core/trycycler/subsample/tests/main.nf.test.snap @@ -0,0 +1,175 @@ +{ + "candidatus_portiera_aleyrodidarum - stub, no ext args": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "sample_01.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_02.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_03.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_04.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_05.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_06.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_07.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_08.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_09.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_10.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_11.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_12.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,74011f3fee0925e1663401586c47ff40" + ], + "subreads": [ + [ + { + "id": "test" + }, + [ + "sample_01.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_02.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_03.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_04.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_05.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_06.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_07.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_08.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_09.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_10.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_11.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "sample_12.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,74011f3fee0925e1663401586c47ff40" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.10.1" + }, + "timestamp": "2024-05-22T11:55:39.51526623" + }, + "candidatus_portiera_aleyrodidarum - 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"modules/nf-core/trycycler/subsample/**"