From caffbfa9e998603e25ae1e5d0ed071dc574e947f Mon Sep 17 00:00:00 2001 From: Gaelle Marenne Date: Fri, 13 Mar 2026 12:54:43 +0100 Subject: [PATCH 1/5] topic migration crispresso2 --- modules/nf-core/crispresso2/main.nf | 12 +-- modules/nf-core/crispresso2/meta.yml | 41 ++++++---- .../nf-core/crispresso2/tests/main.nf.test | 32 ++++---- .../crispresso2/tests/main.nf.test.snap | 75 +++++++++++++++++-- 4 files changed, 115 insertions(+), 45 deletions(-) diff --git a/modules/nf-core/crispresso2/main.nf b/modules/nf-core/crispresso2/main.nf index 343367cc755f..f63ccdd9e284 100644 --- a/modules/nf-core/crispresso2/main.nf +++ b/modules/nf-core/crispresso2/main.nf @@ -14,7 +14,7 @@ process CRISPRESSO2 { tuple val(meta), path("CRISPResso_on_*") , emit: results tuple val(meta), path("*.html") , emit: html tuple val(meta), path("CRISPResso_on_*/*.txt") , emit: txt - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('crispresso2'), eval("CRISPResso --version 2>&1 | sed 's/CRISPResso //'"), emit: versions_crispresso2, topic: versions when: task.ext.when == null || task.ext.when @@ -37,11 +37,6 @@ process CRISPRESSO2 { --name ${prefix} \\ --output_folder . \\ ${args} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - crispresso2: \$(CRISPResso --version 2>&1 | grep -o 'CRISPResso version [0-9.]*' | sed 's/CRISPResso version //') - END_VERSIONS """ stub: @@ -56,10 +51,5 @@ process CRISPRESSO2 { touch CRISPResso_on_${prefix}/CRISPResso_mapping_statistics.txt touch CRISPResso_on_${prefix}/quantification_of_editing_frequency.txt touch ${prefix}.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - crispresso2: 2.3.3 - END_VERSIONS """ } diff --git a/modules/nf-core/crispresso2/meta.yml b/modules/nf-core/crispresso2/meta.yml index 1e4b2a84284f..4569a40602ad 100644 --- a/modules/nf-core/crispresso2/meta.yml +++ b/modules/nf-core/crispresso2/meta.yml @@ -1,4 +1,3 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crispresso2" description: "A software pipeline for the analysis of genome editing outcomes from deep sequencing data" @@ -15,9 +14,9 @@ tools: documentation: "https://docs.crispresso.com" tool_dev_url: "https://github.com/pinellolab/CRISPResso2" doi: "10.1038/s41587-019-0032-3" - licence: ["MIT"] + licence: + - "MIT" identifier: biotools:crispresso2 - input: - - meta: type: map @@ -30,8 +29,7 @@ input: paired-end data, respectively. pattern: "*.{fastq,fq,fastq.gz,fq.gz}" ontologies: - - edam: http://edamontology.org/format_1930 # FASTQ - + - edam: http://edamontology.org/format_1930 output: results: - - meta: @@ -54,27 +52,40 @@ output: description: CRISPResso HTML report pattern: "*.html" ontologies: - - edam: http://edamontology.org/format_2331 # HTML + - edam: http://edamontology.org/format_2331 txt: - - meta: type: map description: | Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]` - - "CRISPResso_on_*/*.txt": + - CRISPResso_on_*/*.txt: type: file description: CRISPResso text output files pattern: "CRISPResso_on_*/*.txt" ontologies: - - edam: http://edamontology.org/format_2330 # Textual format + - edam: http://edamontology.org/format_2330 + versions_crispresso2: + - - ${task.process}: + type: string + description: The name of the process + - crispresso2: + type: string + description: The name of the tool + - CRISPResso --version 2>&1 | sed 's/CRISPResso //': + type: eval + description: The expression to obtain the version of the tool +topics: versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" - - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + - - ${task.process}: + type: string + description: The name of the process + - crispresso2: + type: string + description: The name of the tool + - CRISPResso --version 2>&1 | sed 's/CRISPResso //': + type: eval + description: The expression to obtain the version of the tool authors: - "@sathyasjali" maintainers: diff --git a/modules/nf-core/crispresso2/tests/main.nf.test b/modules/nf-core/crispresso2/tests/main.nf.test index da400ccbbb4e..c3aab4b86640 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test +++ b/modules/nf-core/crispresso2/tests/main.nf.test @@ -24,12 +24,14 @@ nextflow_process { } then { - assertAll( + assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("single_end_versions") }, - { assert process.out.results[0][1].size() > 0 }, - { assert process.out.html[0][1].size() > 0 }, - { assert process.out.txt[0][1].size() > 0 } + { assert snapshot( + process.out.results[0][1].size(), + process.out.html[0][1].size(), + process.out.txt[0][1].size(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() }, ) } } @@ -55,10 +57,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("paired_end_versions") }, - { assert process.out.results[0][1].size() > 0 }, - { assert process.out.html[0][1].size() > 0 }, - { assert process.out.txt[0][1].size() > 0 } + { assert snapshot( + process.out.results[0][1].size(), + process.out.html[0][1].size(), + process.out.txt[0][1].size(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() }, ) } } @@ -81,10 +85,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("nhej_analysis_versions") }, - { assert process.out.results[0][1].size() > 0 }, - { assert process.out.html[0][1].size() > 0 }, - { assert process.out.txt[0][1].size() > 0 } + { assert snapshot( + process.out.results[0][1].size(), + process.out.html[0][1].size(), + process.out.txt[0][1].size(), + process.out.findAll { key, val -> key.startsWith("versions")} + ).match() }, ) } } diff --git a/modules/nf-core/crispresso2/tests/main.nf.test.snap b/modules/nf-core/crispresso2/tests/main.nf.test.snap index 38236c9efe30..d7bde9e199e5 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test.snap +++ b/modules/nf-core/crispresso2/tests/main.nf.test.snap @@ -5,11 +5,32 @@ "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" ] ], + "timestamp": "2025-09-04T10:40:04.221264", "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" - }, - "timestamp": "2025-09-04T10:40:04.221264" + } + }, + "crispresso2 - paired_end": { + "content": [ + 2, + 2, + 9, + { + "versions_crispresso2": [ + [ + "CRISPRESSO2", + "crispresso2", + "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-w7nzd3rg because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + ] + ] + } + ], + "timestamp": "2026-03-13T12:54:03.124903758", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "nhej_analysis_versions": { "content": [ @@ -17,11 +38,53 @@ "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" ] ], + "timestamp": "2025-09-04T10:40:15.66427", "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" - }, - "timestamp": "2025-09-04T10:40:15.66427" + } + }, + "crispresso2 - nhej_analysis": { + "content": [ + 2, + 172, + 9, + { + "versions_crispresso2": [ + [ + "CRISPRESSO2", + "crispresso2", + "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-7vs67k4u because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + ] + ] + } + ], + "timestamp": "2026-03-13T12:54:17.084865807", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "crispresso2 - single_end": { + "content": [ + 2, + 167, + 9, + { + "versions_crispresso2": [ + [ + "CRISPRESSO2", + "crispresso2", + "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-2ej2e90g because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + ] + ] + } + ], + "timestamp": "2026-03-13T12:53:46.123645526", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } }, "single_end_versions": { "content": [ @@ -29,10 +92,10 @@ "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" ] ], + "timestamp": "2025-09-04T10:39:52.068269", "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" - }, - "timestamp": "2025-09-04T10:39:52.068269" + } } } \ No newline at end of file From 463cb4cc3b0907370f18536f5478ed02e587d5b4 Mon Sep 17 00:00:00 2001 From: Gaelle Marenne Date: Fri, 13 Mar 2026 14:32:22 +0100 Subject: [PATCH 2/5] topic migration crispresso2 --- modules/nf-core/crispresso2/main.nf | 2 ++ modules/nf-core/crispresso2/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/crispresso2/main.nf b/modules/nf-core/crispresso2/main.nf index f63ccdd9e284..8472718df801 100644 --- a/modules/nf-core/crispresso2/main.nf +++ b/modules/nf-core/crispresso2/main.nf @@ -32,6 +32,7 @@ process CRISPRESSO2 { } """ + export MPLCONFIGDIR=.matplotlib CRISPResso \\ ${read_inputs} \\ --name ${prefix} \\ @@ -44,6 +45,7 @@ process CRISPRESSO2 { """ #!/usr/bin/env bash set -e + export MPLCONFIGDIR=.matplotlib mkdir -p CRISPResso_on_${prefix} touch CRISPResso_on_${prefix}/${prefix}.html diff --git a/modules/nf-core/crispresso2/tests/main.nf.test.snap b/modules/nf-core/crispresso2/tests/main.nf.test.snap index d7bde9e199e5..01d69f1b2b7a 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test.snap +++ b/modules/nf-core/crispresso2/tests/main.nf.test.snap @@ -21,7 +21,7 @@ [ "CRISPRESSO2", "crispresso2", - "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-w7nzd3rg because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + "2.3.3" ] ] } @@ -54,7 +54,7 @@ [ "CRISPRESSO2", "crispresso2", - "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-7vs67k4u because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + "2.3.3" ] ] } @@ -75,12 +75,12 @@ [ "CRISPRESSO2", "crispresso2", - "mkdir -p failed for path /home/gmarenne/.config/matplotlib: [Errno 30] Read-only file system: '/home/gmarenne'\nMatplotlib created a temporary cache directory at /tmp/matplotlib-2ej2e90g because there was an issue with the default path (/home/gmarenne/.config/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n2.3.3" + "2.3.3" ] ] } ], - "timestamp": "2026-03-13T12:53:46.123645526", + "timestamp": "2026-03-13T14:30:47.099537858", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From ce661068c9854a1fa6fb406d297f28b5141a219c Mon Sep 17 00:00:00 2001 From: Gaelle Marenne Date: Fri, 13 Mar 2026 15:02:40 +0100 Subject: [PATCH 3/5] topic migration crispresso2 --- .../nf-core/crispresso2/tests/main.nf.test | 6 +- .../crispresso2/tests/main.nf.test.snap | 356 +++++++++++++++++- 2 files changed, 353 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/crispresso2/tests/main.nf.test b/modules/nf-core/crispresso2/tests/main.nf.test index c3aab4b86640..277435bd6149 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test +++ b/modules/nf-core/crispresso2/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.results[0][1].size(), - process.out.html[0][1].size(), + process.out.html[0][1].collect{ html -> file(html).name }.sort(), process.out.txt[0][1].size(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() }, @@ -59,7 +59,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.results[0][1].size(), - process.out.html[0][1].size(), + process.out.html[0][1].collect{ html -> file(html).name }.sort(), process.out.txt[0][1].size(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() }, @@ -87,7 +87,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.results[0][1].size(), - process.out.html[0][1].size(), + process.out.html[0][1].collect{ html -> file(html).name }.sort(), process.out.txt[0][1].size(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() }, diff --git a/modules/nf-core/crispresso2/tests/main.nf.test.snap b/modules/nf-core/crispresso2/tests/main.nf.test.snap index 01d69f1b2b7a..75170561830d 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test.snap +++ b/modules/nf-core/crispresso2/tests/main.nf.test.snap @@ -14,7 +14,10 @@ "crispresso2 - paired_end": { "content": [ 2, - 2, + [ + "CRISPResso_on_paired_test.html", + "fastp.html" + ], 9, { "versions_crispresso2": [ @@ -26,7 +29,7 @@ ] } ], - "timestamp": "2026-03-13T12:54:03.124903758", + "timestamp": "2026-03-13T14:56:09.120398517", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -47,7 +50,180 @@ "crispresso2 - nhej_analysis": { "content": [ 2, - 172, + [ + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "-", + ".", + ".", + "0", + "0", + "0", + "0", + "1", + "1", + "1", + "1", + "2", + "2", + "2", + "2", + "2", + "2", + "2", + "3", + "3", + "3", + "3", + "3", + "4", + "4", + "4", + "4", + "4", + "5", + "5", + "5", + "6", + "7", + "8", + "8", + "8", + "9", + "9", + "9", + "9", + "9", + "9", + "9", + "9", + "C", + "C", + "D", + "E", + "G", + "H", + "I", + "I", + "I", + "K", + "N", + "O", + "O", + "P", + "R", + "R", + "R", + "R", + "R", + "S", + "T", + "W", + "Y", + "_", + "_", + "_", + "_", + "_", + "_", + "a", + "a", + "a", + "a", + "a", + "a", + "a", + "a", + "b", + "b", + "b", + "b", + "b", + "c", + "c", + "c", + "c", + "c", + "c", + "c", + "c", + "c", + "d", + "d", + "d", + "d", + "d", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "f", + "f", + "f", + "f", + "f", + "g", + "h", + "h", + "j", + "k", + "k", + "l", + "l", + "m", + "m", + "m", + "n", + "n", + "n", + "n", + "n", + "n", + "n", + "o", + "o", + "o", + "o", + "o", + "o", + "r", + "r", + "r", + "s", + "s", + "s", + "s", + "s", + "s", + "s", + "t", + "t", + "t", + "t", + "t", + "t", + "t", + "t", + "u", + "w" + ], 9, { "versions_crispresso2": [ @@ -59,7 +235,7 @@ ] } ], - "timestamp": "2026-03-13T12:54:17.084865807", + "timestamp": "2026-03-13T14:58:20.823551976", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -68,7 +244,175 @@ "crispresso2 - single_end": { "content": [ 2, - 167, + [ + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "-", + ".", + ".", + "0", + "0", + "0", + "0", + "0", + "0", + "1", + "1", + "1", + "1", + "2", + "2", + "2", + "2", + "3", + "3", + "4", + "4", + "4", + "4", + "5", + "5", + "5", + "5", + "5", + "5", + "6", + "6", + "6", + "7", + "7", + "7", + "7", + "8", + "8", + "8", + "8", + "9", + "9", + "9", + "9", + "C", + "C", + "D", + "E", + "G", + "H", + "I", + "I", + "I", + "K", + "N", + "O", + "O", + "P", + "R", + "R", + "R", + "R", + "R", + "S", + "T", + "W", + "Y", + "_", + "_", + "_", + "_", + "_", + "a", + "a", + "a", + "a", + "a", + "a", + "b", + "b", + "b", + "b", + "b", + "c", + "c", + "c", + "d", + "d", + "d", + "d", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "e", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "f", + "g", + "h", + "k", + "k", + "l", + "l", + "m", + "m", + "m", + "n", + "n", + "n", + "n", + "n", + "n", + "o", + "o", + "o", + "o", + "o", + "o", + "r", + "r", + "r", + "s", + "s", + "s", + "s", + "s", + "s", + "s", + "t", + "t", + "t", + "t", + "t", + "t", + "t", + "t", + "u", + "w" + ], 9, { "versions_crispresso2": [ @@ -80,7 +424,7 @@ ] } ], - "timestamp": "2026-03-13T14:30:47.099537858", + "timestamp": "2026-03-13T14:54:40.546659246", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From e604af9135295e97bc9f383f9f346539d7260ab6 Mon Sep 17 00:00:00 2001 From: Gaelle Marenne Date: Fri, 13 Mar 2026 15:36:10 +0100 Subject: [PATCH 4/5] topic migration crispresso2 --- .../nf-core/crispresso2/tests/main.nf.test | 4 +- .../crispresso2/tests/main.nf.test.snap | 385 +----------------- 2 files changed, 6 insertions(+), 383 deletions(-) diff --git a/modules/nf-core/crispresso2/tests/main.nf.test b/modules/nf-core/crispresso2/tests/main.nf.test index 277435bd6149..124976921f15 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test +++ b/modules/nf-core/crispresso2/tests/main.nf.test @@ -28,7 +28,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.results[0][1].size(), - process.out.html[0][1].collect{ html -> file(html).name }.sort(), + file(process.out.html[0][1]).name, process.out.txt[0][1].size(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() }, @@ -87,7 +87,7 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.results[0][1].size(), - process.out.html[0][1].collect{ html -> file(html).name }.sort(), + file(process.out.html[0][1]).name, process.out.txt[0][1].size(), process.out.findAll { key, val -> key.startsWith("versions")} ).match() }, diff --git a/modules/nf-core/crispresso2/tests/main.nf.test.snap b/modules/nf-core/crispresso2/tests/main.nf.test.snap index 75170561830d..7b656b4a21aa 100644 --- a/modules/nf-core/crispresso2/tests/main.nf.test.snap +++ b/modules/nf-core/crispresso2/tests/main.nf.test.snap @@ -1,16 +1,4 @@ { - "paired_end_versions": { - "content": [ - [ - "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" - ] - ], - "timestamp": "2025-09-04T10:40:04.221264", - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - } - }, "crispresso2 - paired_end": { "content": [ 2, @@ -35,195 +23,10 @@ "nextflow": "25.10.4" } }, - "nhej_analysis_versions": { - "content": [ - [ - "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" - ] - ], - "timestamp": "2025-09-04T10:40:15.66427", - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - } - }, "crispresso2 - nhej_analysis": { "content": [ 2, - [ - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "-", - ".", - ".", - "0", - "0", - "0", - "0", - "1", - "1", - "1", - "1", - "2", - "2", - "2", - "2", - "2", - "2", - "2", - "3", - "3", - "3", - "3", - "3", - "4", - "4", - "4", - "4", - "4", - "5", - "5", - "5", - "6", - "7", - "8", - "8", - "8", - "9", - "9", - "9", - "9", - "9", - "9", - "9", - "9", - "C", - "C", - "D", - "E", - "G", - "H", - "I", - "I", - "I", - "K", - "N", - "O", - "O", - "P", - "R", - "R", - "R", - "R", - "R", - "S", - "T", - "W", - "Y", - "_", - "_", - "_", - "_", - "_", - "_", - "a", - "a", - "a", - "a", - "a", - "a", - "a", - "a", - "b", - "b", - "b", - "b", - "b", - "c", - "c", - "c", - "c", - "c", - "c", - "c", - "c", - "c", - "d", - "d", - "d", - "d", - "d", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "f", - "f", - "f", - "f", - "f", - "g", - "h", - "h", - "j", - "k", - "k", - "l", - "l", - "m", - "m", - "m", - "n", - "n", - "n", - "n", - "n", - "n", - "n", - "o", - "o", - "o", - "o", - "o", - "o", - "r", - "r", - "r", - "s", - "s", - "s", - "s", - "s", - "s", - "s", - "t", - "t", - "t", - "t", - "t", - "t", - "t", - "t", - "u", - "w" - ], + "CRISPResso_on_nhej_test.html", 9, { "versions_crispresso2": [ @@ -235,7 +38,7 @@ ] } ], - "timestamp": "2026-03-13T14:58:20.823551976", + "timestamp": "2026-03-13T15:34:17.493407027", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -244,175 +47,7 @@ "crispresso2 - single_end": { "content": [ 2, - [ - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "", - "-", - ".", - ".", - "0", - "0", - "0", - "0", - "0", - "0", - "1", - "1", - "1", - "1", - "2", - "2", - "2", - "2", - "3", - "3", - "4", - "4", - "4", - "4", - "5", - "5", - "5", - "5", - "5", - "5", - "6", - "6", - "6", - "7", - "7", - "7", - "7", - "8", - "8", - "8", - "8", - "9", - "9", - "9", - "9", - "C", - "C", - "D", - "E", - "G", - "H", - "I", - "I", - "I", - "K", - "N", - "O", - "O", - "P", - "R", - "R", - "R", - "R", - "R", - "S", - "T", - "W", - "Y", - "_", - "_", - "_", - "_", - "_", - "a", - "a", - "a", - "a", - "a", - "a", - "b", - "b", - "b", - "b", - "b", - "c", - "c", - "c", - "d", - "d", - "d", - "d", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "e", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "f", - "g", - "h", - "k", - "k", - "l", - "l", - "m", - "m", - "m", - "n", - "n", - "n", - "n", - "n", - "n", - "o", - "o", - "o", - "o", - "o", - "o", - "r", - "r", - "r", - "s", - "s", - "s", - "s", - "s", - "s", - "s", - "t", - "t", - "t", - "t", - "t", - "t", - "t", - "t", - "u", - "w" - ], + "CRISPResso_on_test.html", 9, { "versions_crispresso2": [ @@ -424,22 +59,10 @@ ] } ], - "timestamp": "2026-03-13T14:54:40.546659246", + "timestamp": "2026-03-13T15:32:17.852481198", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" } - }, - "single_end_versions": { - "content": [ - [ - "versions.yml:md5,2c04a720d2ac80a8651db90eaa1e8c35" - ] - ], - "timestamp": "2025-09-04T10:39:52.068269", - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - } } } \ No newline at end of file From 1791b36cf84a8ec2c915109cb5cc294535477d97 Mon Sep 17 00:00:00 2001 From: Gaelle Marenne Date: Mon, 16 Mar 2026 14:45:08 +0100 Subject: [PATCH 5/5] topic migration crispresso2 --- modules/nf-core/crispresso2/environment.yml | 5 ++++- modules/nf-core/crispresso2/meta.yml | 7 ++++--- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/crispresso2/environment.yml b/modules/nf-core/crispresso2/environment.yml index 58b7db0733da..af544d050c73 100644 --- a/modules/nf-core/crispresso2/environment.yml +++ b/modules/nf-core/crispresso2/environment.yml @@ -4,4 +4,7 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::crispresso2=2.3.3" + - bioconda::bowtie2=2.5.4 + - bioconda::crispresso2=2.3.3 + - bioconda::fastp=1.0.1 + - bioconda::samtools=1.22 diff --git a/modules/nf-core/crispresso2/meta.yml b/modules/nf-core/crispresso2/meta.yml index 4569a40602ad..2d8a1fff4883 100644 --- a/modules/nf-core/crispresso2/meta.yml +++ b/modules/nf-core/crispresso2/meta.yml @@ -1,3 +1,4 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crispresso2" description: "A software pipeline for the analysis of genome editing outcomes from deep sequencing data" @@ -29,7 +30,7 @@ input: paired-end data, respectively. pattern: "*.{fastq,fq,fastq.gz,fq.gz}" ontologies: - - edam: http://edamontology.org/format_1930 + - edam: http://edamontology.org/format_1930 # FASTQ output: results: - - meta: @@ -52,7 +53,7 @@ output: description: CRISPResso HTML report pattern: "*.html" ontologies: - - edam: http://edamontology.org/format_2331 + - edam: http://edamontology.org/format_2331 # HTML txt: - - meta: type: map @@ -64,7 +65,7 @@ output: description: CRISPResso text output files pattern: "CRISPResso_on_*/*.txt" ontologies: - - edam: http://edamontology.org/format_2330 + - edam: http://edamontology.org/format_2330 # Textual format versions_crispresso2: - - ${task.process}: type: string