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* Initial addition * Updated snapshot * Updated snapshot * Updated tests. * Updated tests. * Updated snapshot * removed extra directory creation * Added plugin to only compare bam reads, not header * Added plugin to only compare bam reads, not header * Added plugin to only compare bam reads, not header * Output filename now also contains index id so as to not to repeat filenames * Updated snapshot * Updated snapshot * Added paired end test * Added paired end test * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated tests to deal with bams changing order of reads each time * Updated container used * Added number of lines test for review * Added number of lines test for review * Updated nft-bam plugin * Updated container * Updated counting of reads * Updated counting of reads * removed * updated snapshot * Updated test and snapshot * Updated test and snapshot * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * fixed versions issue * Updated test * Updated test * Updated snapshot * Updated tag * Updated tests * Updated tests * Improved descriptions --------- Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Igor Trujnara <53370556+itrujnara@users.noreply.github.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::coptr=1.1.4" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| process COPTR_MAP { | ||
| tag "$meta.id" | ||
| label 'process_low' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/coptr:1.1.4--pyhdfd78af_3': | ||
| 'biocontainers/coptr:1.1.4--pyhdfd78af_3' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(fasta, stageAs: "fastafolder/*") | ||
| tuple val(meta2), path(index) | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.bam"), emit: bam | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def prefix2 = task.ext.prefix ?: "${meta2.id}" | ||
|
|
||
| def paired_end = "" | ||
| if ( ! meta.single_end ) { | ||
| paired_end = "--paired" | ||
| } | ||
| """ | ||
| INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"` | ||
| [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"` | ||
| [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1 | ||
| coptr \ | ||
| map \ | ||
| $args $paired_end \ | ||
| --threads $task.cpus \ | ||
| \$INDEX \ | ||
| fastafolder \ | ||
| . | ||
| mv ${prefix}.bam ${prefix}_${prefix2}.bam | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/') | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| """ | ||
| touch ${prefix}.bam | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| coptr: \$(coptr |& sed -E '11!d ; s/CoPTR.*?\\(v(.*?)\\).*/\\1/') | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| --- | ||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | ||
| name: "coptr_map" | ||
| description: Maps the reads to the reference database | ||
| keywords: | ||
| - coptr | ||
| - mapping | ||
| - ptr | ||
| tools: | ||
| - "coptr": | ||
| description: "Accurate and robust inference of microbial growth dynamics from | ||
| metagenomic sequencing reads." | ||
| homepage: "https://github.com/tyjo/coptr" | ||
| documentation: "https://coptr.readthedocs.io/" | ||
| tool_dev_url: "https://github.com/tyjo/coptr" | ||
| doi: "10.1101/gr.275533.121" | ||
| licence: ["GPL v3"] | ||
| identifier: biotools:coptr | ||
|
|
||
| input: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - fasta: | ||
| type: file | ||
| description: fastq file with reads | ||
| pattern: "*.{.fastq,.fq,.fastq.gz,fq.gz}" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_1929" | ||
| - - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing index genome id and path | ||
| e.g. [ id:'test', 'bowtie2' ] | ||
| - index: | ||
| type: file | ||
| description: Directory with Bowtie2 genome index files | ||
| pattern: "*.ebwt" | ||
|
|
||
| output: | ||
| - bam: | ||
| - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - "*.bam": | ||
| type: file | ||
| description: Alignment (BAM) file of reads mapped to the reference database | ||
| pattern: "*.{bam}" | ||
| ontologies: | ||
| - edam: "http://edamontology.org/format_2572" | ||
| - versions: | ||
| - "versions.yml": | ||
| type: file | ||
| description: File containing software versions | ||
| pattern: "versions.yml" | ||
| authors: | ||
| - "@ramirobarrantes" | ||
| maintainers: | ||
| - "@ramirobarrantes" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process COPTR_MAP" | ||
| script "../main.nf" | ||
| process "COPTR_MAP" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "coptr" | ||
| tag "coptr/index" | ||
| tag "coptr/map" | ||
|
|
||
| setup { | ||
| run("COPTR_INDEX") { | ||
| script "../../index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [id:'test_0'], | ||
| file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
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| test("sarscov2 - single end test") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test_1', single_end: true ], | ||
| file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) | ||
| ] | ||
| input[1] = COPTR_INDEX.out.index_dir | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.bam.collect{bam(it[1]).getReads(10)}, | ||
| process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])}, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("sarscov2 - paired end") { | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end: false ], | ||
| [ | ||
| 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) | ||
| ] | ||
| ] | ||
| input[1] = COPTR_INDEX.out.index_dir | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out.bam.collect{bam(it[1]).getStatistics(include:["readCount"])}, | ||
| process.out.versions | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
|
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|
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| test("sarscov2 - single end - stub") { | ||
|
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| options "-stub" | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test', single_end: true ], | ||
| file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) | ||
| ] | ||
| input[1] = COPTR_INDEX.out.index_dir | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| } |
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