From d8bfba2e0d165d0340034d1bb8b68744b40e1f71 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 13:45:32 +0000 Subject: [PATCH 1/6] change module structure and test --- subworkflows/local/trim_subworkflow/main.nf | 46 +++++++++++++++++ .../local/trim_subworkflow/tests/main.nf.test | 50 +++++++++++++++++++ subworkflows/local/trim_workflow.nf | 42 ---------------- workflows/rnafusion.nf | 41 ++++++++------- 4 files changed, 119 insertions(+), 60 deletions(-) create mode 100644 subworkflows/local/trim_subworkflow/main.nf create mode 100644 subworkflows/local/trim_subworkflow/tests/main.nf.test delete mode 100644 subworkflows/local/trim_workflow.nf diff --git a/subworkflows/local/trim_subworkflow/main.nf b/subworkflows/local/trim_subworkflow/main.nf new file mode 100644 index 00000000..2cbb8380 --- /dev/null +++ b/subworkflows/local/trim_subworkflow/main.nf @@ -0,0 +1,46 @@ + + +include { FASTP } from '../../../modules/nf-core/fastp/main' +include { FASTQC as FASTQC_FOR_FASTP } from '../../../modules/nf-core/fastqc/main' + +workflow TRIM_WORKFLOW { + + take: + reads // channel [ meta, [ fastqs ] ] + adapter_fasta // channel [ path ] + fastp_trim // boolean + + main: + ch_versions = Channel.empty() + ch_fastp_html = Channel.empty() + ch_fastp_json = Channel.empty() + ch_fastqc_trimmed = Channel.empty() + + if ( fastp_trim ) { + FASTP(reads, adapter_fasta.ifEmpty( [] ), false, false, false) + ch_versions = ch_versions.mix(FASTP.out.versions) + + FASTQC_FOR_FASTP(FASTP.out.reads) + ch_versions = ch_versions.mix(FASTQC_FOR_FASTP.out.versions) + + ch_reads_all = FASTP.out.reads + ch_reads_fusioncatcher = ch_reads_all + ch_fastp_html = FASTP.out.html + ch_fastp_json = FASTP.out.json + ch_fastqc_trimmed = FASTQC_FOR_FASTP.out.zip + + } + else { + ch_reads_all = reads + ch_reads_fusioncatcher = reads + } + + emit: + ch_reads_all // Channel [ meta, [reads] ] + ch_reads_fusioncatcher // Channel [ meta, [reads] ] + ch_fastp_html // Channel [ meta, path_html ] + ch_fastp_json // Channel [ meta, path_json ] + ch_fastqc_trimmed // Channel [ meta, path_zip ] + versions = ch_versions // Channel [ versions ] + } + diff --git a/subworkflows/local/trim_subworkflow/tests/main.nf.test b/subworkflows/local/trim_subworkflow/tests/main.nf.test new file mode 100644 index 00000000..66007f0d --- /dev/null +++ b/subworkflows/local/trim_subworkflow/tests/main.nf.test @@ -0,0 +1,50 @@ +nextflow_workflow { + + name "Test Subworkflow QC_WORKFLOW" + script "../main.nf" + //config "./nextflow.config" + workflow "TRIM_WORKFLOW" + tag "qc" + tag "subworkflow" + + test("TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP true") { + + when { + params { + fastp_trim = true + } + + workflow { + """ + // ch_reads + input[0] = Channel.of( + [ + [id: "test_fastq"], + [ + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ]) + input[1] = Channel.empty() + input[2] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { with(workflow.out) { + assert snapshot( + versions.collect{ file(it) }, + ch_reads_all[0][1].collect { file(it) }, + ch_reads_fusioncatcher[0][1].collect { file(it) }, + file(ch_fastp_html[0][1]).name, + file(ch_fastp_json[0][1]), + ch_fastqc_trimmed[0][1].collect { file(it).name } + ).match() } + } + ) + } + } +} diff --git a/subworkflows/local/trim_workflow.nf b/subworkflows/local/trim_workflow.nf deleted file mode 100644 index 27088a18..00000000 --- a/subworkflows/local/trim_workflow.nf +++ /dev/null @@ -1,42 +0,0 @@ -include { FASTP } from '../../modules/nf-core/fastp/main' -include { FASTQC as FASTQC_FOR_FASTP } from '../../modules/nf-core/fastqc/main' - - -workflow TRIM_WORKFLOW { - take: - reads - - main: - ch_versions = Channel.empty() - ch_fastp_html = Channel.empty() - ch_fastp_json = Channel.empty() - ch_fastqc_trimmed = Channel.empty() - - if (params.fastp_trim) { - FASTP(reads, params.adapter_fasta, false, false, false) - ch_versions = ch_versions.mix(FASTP.out.versions) - - FASTQC_FOR_FASTP(FASTP.out.reads) - ch_versions = ch_versions.mix(FASTQC_FOR_FASTP.out.versions) - - ch_reads_all = FASTP.out.reads - ch_reads_fusioncatcher = ch_reads_all - ch_fastp_html = FASTP.out.html - ch_fastp_json = FASTP.out.json - ch_fastqc_trimmed = FASTQC_FOR_FASTP.out.zip - - } - else { - ch_reads_all = reads - ch_reads_fusioncatcher = reads - } - - emit: - ch_reads_all - ch_reads_fusioncatcher - ch_fastp_html - ch_fastp_json - ch_fastqc_trimmed - versions = ch_versions - } - diff --git a/workflows/rnafusion.nf b/workflows/rnafusion.nf index 1f7890b5..bafea68c 100644 --- a/workflows/rnafusion.nf +++ b/workflows/rnafusion.nf @@ -22,23 +22,25 @@ include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pi include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_rnafusion_pipeline' -ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() -ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() -ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() -ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() -ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() -ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() -ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect() -ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect() +ch_chrgtf = params.starfusion_build ? Channel.fromPath(params.chrgtf).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_annot.gtf").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ref = params.starfusion_build ? Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.starfusion_ref}/ref_genome.fa.star.idx").map { it -> [[id:it.Name], it] }.collect() +ch_starindex_ensembl_ref = Channel.fromPath(params.starindex_ref).map { it -> [[id:it.Name], it] }.collect() +ch_refflat = params.starfusion_build ? Channel.fromPath(params.refflat).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.gtf.refflat").map { it -> [[id:it.Name], it] }.collect() +ch_rrna_interval = params.starfusion_build ? Channel.fromPath(params.rrna_intervals).map { it -> [[id:it.Name], it] }.collect() : Channel.fromPath("${params.ensembl_ref}/ref_annot.interval_list").map { it -> [[id:it.Name], it] }.collect() +ch_adapter_fastp = params.adapter_fasta ? Channel.fromPath(params.adapter_fasta, checkIfExists: true) : Channel.empty() +ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_blacklist = Channel.fromPath(params.arriba_ref_blacklist).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_known_fusions = Channel.fromPath(params.arriba_ref_known_fusions).map { it -> [[id:it.Name], it] }.collect() ch_arriba_ref_protein_domains = Channel.fromPath(params.arriba_ref_protein_domains).map { it -> [[id:it.Name], it] }.collect() -ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect() -ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { it -> [[id:it.Name], it] }.collect() -ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { it -> [[id:it.Name], it] }.collect() -ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() -ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() +ch_arriba_ref_cytobands = Channel.fromPath(params.arriba_ref_cytobands).map { it -> [[id:it.Name], it] }.collect() +ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { it -> [[id:it.Name], it] }.collect() +ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { it -> [[id:it.Name], it] }.collect() +ch_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it.Name], it] }.collect() +ch_gtf = Channel.fromPath(params.gtf).map { it -> [[id:it.Name], it] }.collect() ch_salmon_index = Channel.fromPath(params.salmon_index).map { it -> [[id:it.Name], it] }.collect() -ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() -ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() +ch_transcript = Channel.fromPath(params.transcript).map { it -> [[id:it.Name], it] }.collect() +ch_fai = Channel.fromPath(params.fai).map { it -> [[id:it.Name], it] }.collect() + /* @@ -51,6 +53,7 @@ workflow RNAFUSION { take: ch_samplesheet // channel: samplesheet read in from --input + main: ch_versions = Channel.empty() @@ -67,11 +70,13 @@ workflow RNAFUSION { TRIM_WORKFLOW ( - ch_samplesheet + ch_samplesheet, + ch_adapter_fastp, + params.fastp_trim ) ch_reads_fusioncatcher = TRIM_WORKFLOW.out.ch_reads_fusioncatcher - ch_reads_all = TRIM_WORKFLOW.out.ch_reads_all - ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions) + ch_reads_all = TRIM_WORKFLOW.out.ch_reads_all + ch_versions = ch_versions.mix(TRIM_WORKFLOW.out.versions) SALMON_QUANT( ch_reads_all, ch_salmon_index.map{ meta, index -> index }, ch_gtf.map{ meta, gtf -> gtf }, [], false, 'A') From 06ba247e6e624ff95aba80b65b90a09436ab419c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 13:45:53 +0000 Subject: [PATCH 2/6] create snap --- .../trim_subworkflow/tests/main.nf.test.snap | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 subworkflows/local/trim_subworkflow/tests/main.nf.test.snap diff --git a/subworkflows/local/trim_subworkflow/tests/main.nf.test.snap b/subworkflows/local/trim_subworkflow/tests/main.nf.test.snap new file mode 100644 index 00000000..4623a393 --- /dev/null +++ b/subworkflows/local/trim_subworkflow/tests/main.nf.test.snap @@ -0,0 +1,29 @@ +{ + "TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP true": { + "content": [ + [ + "versions.yml:md5,16187796d989b6260f572247e7dc0fc6", + "versions.yml:md5,ea42abe9875f41f8362a55ee7533f102" + ], + [ + "test_fastq_1.fastp.fastq.gz:md5,0c436583301dea48755a5252a2675b64", + "test_fastq_2.fastp.fastq.gz:md5,f7f38138255e63b33286b819b6177612" + ], + [ + "test_fastq_1.fastp.fastq.gz:md5,0c436583301dea48755a5252a2675b64", + "test_fastq_2.fastp.fastq.gz:md5,f7f38138255e63b33286b819b6177612" + ], + "test_fastq.fastp.html", + "test_fastq.fastp.json:md5,62066ad48c3d5981045cdd43e354cb2b", + [ + "test_fastq_trimmed_1_fastqc.zip", + "test_fastq_trimmed_2_fastqc.zip" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-05T13:42:33.340326167" + } +} \ No newline at end of file From ea4487f0595c1f1d6baf850fd6b7db2d04c58e4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 13:53:28 +0000 Subject: [PATCH 3/6] fix folder name --- subworkflows/local/{trim_subworkflow => trim_workflow}/main.nf | 0 .../local/{trim_subworkflow => trim_workflow}/tests/main.nf.test | 0 .../{trim_subworkflow => trim_workflow}/tests/main.nf.test.snap | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename subworkflows/local/{trim_subworkflow => trim_workflow}/main.nf (100%) rename subworkflows/local/{trim_subworkflow => trim_workflow}/tests/main.nf.test (100%) rename subworkflows/local/{trim_subworkflow => trim_workflow}/tests/main.nf.test.snap (100%) diff --git a/subworkflows/local/trim_subworkflow/main.nf b/subworkflows/local/trim_workflow/main.nf similarity index 100% rename from subworkflows/local/trim_subworkflow/main.nf rename to subworkflows/local/trim_workflow/main.nf diff --git a/subworkflows/local/trim_subworkflow/tests/main.nf.test b/subworkflows/local/trim_workflow/tests/main.nf.test similarity index 100% rename from subworkflows/local/trim_subworkflow/tests/main.nf.test rename to subworkflows/local/trim_workflow/tests/main.nf.test diff --git a/subworkflows/local/trim_subworkflow/tests/main.nf.test.snap b/subworkflows/local/trim_workflow/tests/main.nf.test.snap similarity index 100% rename from subworkflows/local/trim_subworkflow/tests/main.nf.test.snap rename to subworkflows/local/trim_workflow/tests/main.nf.test.snap From e033e9445a20a807651299d0b85c90de2eb441da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 14:25:55 +0000 Subject: [PATCH 4/6] update test for skipping fastp --- .../local/trim_workflow/tests/main.nf.test | 43 +++++++++++++++++-- .../trim_workflow/tests/main.nf.test.snap | 17 +++++++- 2 files changed, 55 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/trim_workflow/tests/main.nf.test b/subworkflows/local/trim_workflow/tests/main.nf.test index 66007f0d..854f9d4d 100644 --- a/subworkflows/local/trim_workflow/tests/main.nf.test +++ b/subworkflows/local/trim_workflow/tests/main.nf.test @@ -2,7 +2,6 @@ nextflow_workflow { name "Test Subworkflow QC_WORKFLOW" script "../main.nf" - //config "./nextflow.config" workflow "TRIM_WORKFLOW" tag "qc" tag "subworkflow" @@ -10,9 +9,6 @@ nextflow_workflow { test("TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP true") { when { - params { - fastp_trim = true - } workflow { """ @@ -47,4 +43,43 @@ nextflow_workflow { ) } } + + test("TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP false") { + + when { + + workflow { + """ + // ch_reads + input[0] = Channel.of( + [ + [id: "test_fastq"], + [ + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ]) + input[1] = Channel.empty() + input[2] = false + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { with(workflow.out) { + assert snapshot( + versions.size() == 0, + ch_reads_all[0][1].size() == 2, + ch_reads_fusioncatcher[0][1].size() == 2, + ch_fastp_html.size() == 0, + ch_fastp_json.size() == 0, + ch_fastqc_trimmed.size() == 0 + ).match() } + } + ) + } + } + } diff --git a/subworkflows/local/trim_workflow/tests/main.nf.test.snap b/subworkflows/local/trim_workflow/tests/main.nf.test.snap index 4623a393..c119f750 100644 --- a/subworkflows/local/trim_workflow/tests/main.nf.test.snap +++ b/subworkflows/local/trim_workflow/tests/main.nf.test.snap @@ -24,6 +24,21 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T13:42:33.340326167" + "timestamp": "2024-12-05T14:11:12.374063253" + }, + "TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP false": { + "content": [ + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-05T14:21:42.396615145" } } \ No newline at end of file From 8f3c70e091df4f0d8f867a11c114ff7f3bd62e9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 14:29:30 +0000 Subject: [PATCH 5/6] update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 11444abe..6a70a434 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551) - Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554) - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560) -- Add nf-test to local subworkflow: `QC_SUBWORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568) +- Add nf-test to local subworkflow: `QC_WORKFLOW` [#568](https://github.com/nf-core/rnafusion/pull/568) +- Add nf-test to local subworkflow: `TRIM_WORKFLOW` [#572](https://github.com/nf-core/rnafusion/pull/572) ### Changed From 90aced2d44603cb0440dd98dd858c0cd87db8f8b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alan=20M=C3=B6bbs?= Date: Thu, 5 Dec 2024 16:24:35 +0000 Subject: [PATCH 6/6] add new test --- .../local/trim_workflow/tests/main.nf.test | 44 ++++++++++++++++++- .../trim_workflow/tests/main.nf.test.snap | 35 +++++++++++++-- 2 files changed, 73 insertions(+), 6 deletions(-) diff --git a/subworkflows/local/trim_workflow/tests/main.nf.test b/subworkflows/local/trim_workflow/tests/main.nf.test index 854f9d4d..2f7568d6 100644 --- a/subworkflows/local/trim_workflow/tests/main.nf.test +++ b/subworkflows/local/trim_workflow/tests/main.nf.test @@ -5,8 +5,10 @@ nextflow_workflow { workflow "TRIM_WORKFLOW" tag "qc" tag "subworkflow" + tag "fastqc" + tag "fastp" - test("TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP true") { + test("TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == true") { when { @@ -44,7 +46,45 @@ nextflow_workflow { } } - test("TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP false") { + test("TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == true + fasp_adaptors") { + + when { + + workflow { + """ + // ch_reads + input[0] = Channel.of( + [ + [id: "test_fastq"], + [ + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz", checkIfExists: true) + ] + ]) + input[1] = Channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/modules/data/delete_me/fastp/adapters.fasta', checkIfExists: true) + input[2] = true + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { with(workflow.out) { + assert snapshot( + versions.collect{ file(it) }, + ch_reads_all[0][1].collect { file(it) }, + ch_reads_fusioncatcher[0][1].collect { file(it) }, + file(ch_fastp_html[0][1]).name, + file(ch_fastp_json[0][1]), + ch_fastqc_trimmed[0][1].collect { file(it).name } + ).match() } + } + ) + } + } + + test("TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == false") { when { diff --git a/subworkflows/local/trim_workflow/tests/main.nf.test.snap b/subworkflows/local/trim_workflow/tests/main.nf.test.snap index c119f750..ae9f9e2e 100644 --- a/subworkflows/local/trim_workflow/tests/main.nf.test.snap +++ b/subworkflows/local/trim_workflow/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP true": { + "TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == true": { "content": [ [ "versions.yml:md5,16187796d989b6260f572247e7dc0fc6", @@ -24,9 +24,9 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T14:11:12.374063253" + "timestamp": "2024-12-05T16:21:52.926289296" }, - "TRIM_WORKFLOW - Homo sapiens - FASTQs - FastP false": { + "TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == false": { "content": [ true, true, @@ -39,6 +39,33 @@ "nf-test": "0.9.0", "nextflow": "24.10.2" }, - "timestamp": "2024-12-05T14:21:42.396615145" + "timestamp": "2024-12-05T16:22:45.877168833" + }, + "TRIM_WORKFLOW - Homo sapiens - FASTQs - fastp == true + fasp_adaptors": { + "content": [ + [ + "versions.yml:md5,16187796d989b6260f572247e7dc0fc6", + "versions.yml:md5,ea42abe9875f41f8362a55ee7533f102" + ], + [ + "test_fastq_1.fastp.fastq.gz:md5,adc67a7b4d0bf3520866d7599a4ba814", + "test_fastq_2.fastp.fastq.gz:md5,9ee7d6c5230442970997477464255e67" + ], + [ + "test_fastq_1.fastp.fastq.gz:md5,adc67a7b4d0bf3520866d7599a4ba814", + "test_fastq_2.fastp.fastq.gz:md5,9ee7d6c5230442970997477464255e67" + ], + "test_fastq.fastp.html", + "test_fastq.fastp.json:md5,feb3483311bfa4ded60146f1cbc13fd5", + [ + "test_fastq_trimmed_1_fastqc.zip", + "test_fastq_trimmed_2_fastqc.zip" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-05T16:22:26.29488483" } } \ No newline at end of file