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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| ERR2537811,s3://pollen-metabarcoding-test-data/data/ERR2537811_1.fastq.gz,s3://pollen-metabarcoding-test-data/data/ERR2537811_2.fastq.gz | ||
| ERR2537812,s3://pollen-metabarcoding-test-data/data/ERR2537812_1.fastq.gz,s3://pollen-metabarcoding-test-data/data/ERR2537812_2.fastq.gz | ||
| ERR2537813,s3://pollen-metabarcoding-test-data/data/ERR2537813_1.fastq.gz,s3://pollen-metabarcoding-test-data/data/ERR2537813_2.fastq.gz | ||
| ERR2537816,ERR2537816 | ||
| ERR2537814,ERR2537814 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| name: sratools_fasterqdump | ||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - bioconda::sra-tools=3.0.8 | ||
| - conda-forge::pigz=2.6 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| process SRATOOLS_FASTERQDUMP { | ||
| tag "$meta.id" | ||
| label 'process_medium' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' : | ||
| 'biocontainers/mulled-v2-5f89fe0cd045cb1d615630b9261a1d17943a9b6a:2f4a4c900edd6801ff0068c2b3048b4459d119eb-0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(sra) | ||
| path ncbi_settings | ||
| path certificate | ||
|
|
||
| output: | ||
| tuple val(meta), path('*.fastq.gz'), emit: reads | ||
| path "versions.yml" , emit: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def outfile = meta.single_end ? "${prefix}.fastq" : prefix | ||
| def key_file = '' | ||
| if (certificate.toString().endsWith('.jwt')) { | ||
| key_file += " --perm ${certificate}" | ||
| } else if (certificate.toString().endsWith('.ngc')) { | ||
| key_file += " --ngc ${certificate}" | ||
| } | ||
| //HAD TO ADD SH SHEBANG TO ENSURE IT WAS INTERPRETED BY RIGHT SHELL, OTHERWISE FAILS WITH "bash not found" ERROR | ||
| //HAD TO CHANGE ${outfile} TO "${outfile}.fastq" TO STOP AN ERROR WHEN WRITING TO THE SAME PLACE AS INPUT FILE | ||
| """ | ||
| #!/bin/sh | ||
| export NCBI_SETTINGS="\$PWD/${ncbi_settings}" | ||
| fasterq-dump \\ | ||
| $args \\ | ||
| --threads $task.cpus \\ | ||
| --outfile "${outfile}.fastq" \\ | ||
| ${key_file} \\ | ||
| ${sra} | ||
| pigz \\ | ||
| $args2 \\ | ||
| --no-name \\ | ||
| --processes $task.cpus \\ | ||
| *.fastq | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+') | ||
| pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| name: sratools_fasterqdump | ||
| description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). | ||
| keywords: | ||
| - sequencing | ||
| - FASTQ | ||
| - dump | ||
| tools: | ||
| - sratools: | ||
| description: SRA Toolkit and SDK from NCBI | ||
| homepage: https://github.com/ncbi/sra-tools | ||
| documentation: https://github.com/ncbi/sra-tools/wiki | ||
| tool_dev_url: https://github.com/ncbi/sra-tools | ||
| licence: ["Public Domain"] | ||
| input: | ||
| - meta: | ||
| type: map | ||
| description: > | ||
| Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | ||
| - sra: | ||
| type: directory | ||
| description: Directory containing ETL data for the given SRA. | ||
| pattern: "*/*.sra" | ||
| - ncbi_settings: | ||
| type: file | ||
| description: > | ||
| An NCBI user settings file. | ||
| pattern: "*.mkfg" | ||
| - certificate: | ||
| type: file | ||
| description: > | ||
| Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit | ||
| pattern: "*.cart" | ||
| 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" | ||
| - reads: | ||
| type: file | ||
| description: Extracted FASTQ file or files if the sequencing reads are paired-end. | ||
| pattern: "*.fastq.gz" | ||
| authors: | ||
| - "@Midnighter" | ||
| maintainers: | ||
| - "@Midnighter" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| nextflow_process { | ||
| name "Test Process SRATOOLS_FASTERQDUMP" | ||
| script "../main.nf" | ||
| config "./nextflow.config" | ||
| process "SRATOOLS_FASTERQDUMP" | ||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "untar" | ||
| tag "sratools" | ||
| tag "sratools/fasterqdump" | ||
|
|
||
| test("Single-end") { | ||
|
|
||
| setup { | ||
| run("UNTAR") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true) ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_single_end', single_end:true ], files]} | ||
| input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) | ||
| input[2] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("Paired-end") { | ||
|
|
||
| setup { | ||
| run("UNTAR") { | ||
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true) ]) | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| when { | ||
| process { | ||
| """ | ||
| input[0] = UNTAR.out.untar.map{ meta, files -> [ [ id:'test_paired_end', single_end:false ], files]} | ||
| input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true) | ||
| input[2] = [] | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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