From fc375d7e0c0e27c7355acdde009fc330b2612019 Mon Sep 17 00:00:00 2001 From: Clara0611 Date: Fri, 13 Mar 2026 11:09:37 +0100 Subject: [PATCH 1/5] new module: stitchr --- modules/nf-core/stitchr/Dockerfile | 26 ++++ modules/nf-core/stitchr/thimble/main.nf | 50 ++++++ modules/nf-core/stitchr/thimble/meta.yml | 104 +++++++++++++ .../stitchr/thimble/tests/main.nf.test | 86 +++++++++++ .../stitchr/thimble/tests/main.nf.test.snap | 144 ++++++++++++++++++ 5 files changed, 410 insertions(+) create mode 100644 modules/nf-core/stitchr/Dockerfile create mode 100644 modules/nf-core/stitchr/thimble/main.nf create mode 100644 modules/nf-core/stitchr/thimble/meta.yml create mode 100644 modules/nf-core/stitchr/thimble/tests/main.nf.test create mode 100644 modules/nf-core/stitchr/thimble/tests/main.nf.test.snap diff --git a/modules/nf-core/stitchr/Dockerfile b/modules/nf-core/stitchr/Dockerfile new file mode 100644 index 000000000000..4ff8b3519012 --- /dev/null +++ b/modules/nf-core/stitchr/Dockerfile @@ -0,0 +1,26 @@ +# ---- Base image ---- +FROM python:3.14 + +LABEL authors="Clara Bierwirth" \ + description="Stitchr container with IMGT human and mouse data" + +# ---- Environment settings ---- +ENV PYTHONDONTWRITEBYTECODE=1 \ + PYTHONUNBUFFERED=1 \ + PATH="/usr/local/bin:${PATH}" + +# ---- System dependencies ---- +RUN apt-get update && apt-get install -y --no-install-recommends \ + git \ + build-essential \ + wget \ + && rm -rf /var/lib/apt/lists/* + +# ---- Install Stitchr and IMGTgeneDL ---- +RUN pip install --no-cache-dir --upgrade --force-reinstall \ + stitchr==1.3.1 \ + IMGTgeneDL==0.6.1 + +# ---- Download human and mouse IMGT data ---- +RUN stitchrdl -s human +RUN stitchrdl -s mouse diff --git a/modules/nf-core/stitchr/thimble/main.nf b/modules/nf-core/stitchr/thimble/main.nf new file mode 100644 index 000000000000..158c0a6df34a --- /dev/null +++ b/modules/nf-core/stitchr/thimble/main.nf @@ -0,0 +1,50 @@ +process STITCHR_THIMBLE { + tag "$meta.id" + label 'process_single' + + + container "ghcr.io/qbic-pipelines/stitchr:1.3.1" + + + input: + tuple val(meta), path(samplesheet) + tuple val(meta2), path(alt_codon_usage) + tuple val(meta3), path(allele_preferences) + val(species) + + + output: + tuple val(meta), path("${meta.id}.tsv"), emit: thimble + tuple val("${task.process}"), val('stitchr'), eval("stitchr --version"), topic: versions, emit: versions_stitchr + tuple val("${task.process}"), val('imgtgenedl'), val("0.6.1"), topic: versions, emit: versions_imgtgenedl + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + //optional files: + def codon_usage = alt_codon_usage ? "-cu ${alt_codon_usage}" : "" + def allele_preference = allele_preferences ? "-p ${allele_preferences}" : "" + + """ + thimble \ + $args \ + -in ${samplesheet} \ + -o ${prefix}.tsv \ + ${codon_usage} \ + ${allele_preference} \ + -s ${species} + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + echo $args + + touch ${prefix}.tsv + """ +} diff --git a/modules/nf-core/stitchr/thimble/meta.yml b/modules/nf-core/stitchr/thimble/meta.yml new file mode 100644 index 000000000000..8e1d7b385e8e --- /dev/null +++ b/modules/nf-core/stitchr/thimble/meta.yml @@ -0,0 +1,104 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "stitchr_thimble" +description: Automatic TCR nucleotide sequence generation from V, J and CDR3 information +keywords: + - TCR + - sequence + - immunology +tools: + - "stitchr": + description: "Automatic TCR nucleotide sequence generation from V, J and CDR3 information" + homepage: "https://github.com/JamieHeather/stitchr" + documentation: "https://jamieheather.github.io/stitchr/index.html" + tool_dev_url: "https://github.com/JamieHeather/stitchr" + doi: "10.1093/nar/gkac190" + licence: ["MIT"] + identifier: "" + - "imgtgenedl": + description: "provides access to TCR and IG genes stored in IMGT/GENE-DB" + homepage: "https://github.com/JamieHeather/IMGTgeneDL" + documentation: "https://github.com/JamieHeather/IMGTgeneDL/blob/main/README.md" + tool_dev_url: "https://github.com/JamieHeather/IMGTgeneDL" + doi: "10.1093/nar/gkab1136" + licence: ["MIT"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - samplesheet: + type: file + description: tsv containing J,V and CDR3 information + pattern: "*.tsv" + ontologies: [] + - alt_codon_usage: + type: file + description: txt containing alternative codon usage in kazusa-like format + pattern: "*.txt" + ontologies: [] + - allele_preferences: + type: file + description: tsv containing alternative allele preferences + pattern: "*.tsv" + ontologies: [] + - species: + type: string + description: Species ("mouse" or "human") + +output: + thimble: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: tsv containing TCR sequence information + pattern: "*.tsv" + ontologies: [] + versions_stitchr: + - - "${task.process}": + type: string + description: The name of the process + - "stitchr": + type: string + description: The name of the tool + - "stitchr --version": + type: eval + description: The expression to obtain the version of the tool + versions_imgtgenedl: + - - "${task.process}": + type: string + description: The name of the process + - "imgtgenedl": + type: string + description: The name of the tool + - "imgtgenedl --version": + type: eval + description: The expression to obtain the version of the tool + +topics: + versions: + - - ${task.process}: + type: string + description: The name of the process + - stitchr: + type: string + description: The name of the tool + - stitchr --version: + type: eval + description: The expression to obtain the version of the tool + - imgtgenedl: + type: string + description: The name of the tool + - imgtgenedl --version: + type: eval + description: The expression to obtain the version of the tool +authors: + - "@Clara0611" +maintainers: + - "@Clara0611" diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test b/modules/nf-core/stitchr/thimble/tests/main.nf.test new file mode 100644 index 000000000000..53e0d755f495 --- /dev/null +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test @@ -0,0 +1,86 @@ +nextflow_process { + + name "Test Process STITCHR_THIMBLE" + script "../main.nf" + process "STITCHR_THIMBLE" + + tag "modules" + tag "modules_nfcore" + tag "stitchr" + tag "stitchr/thimble" + + test("human - tsv") { + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + '', checkIfExists: true), + ] + input[1] = [ + [ id: 'alt_codon_usage' ], + [] + ] + input[2] = [ + [ id: 'allele_preference' ], + [] + ] + input[3] = "human" + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + + test("human - tsv - stub") { + + options "-stub" + + when { + process { + """ + // TODO nf-core: define inputs of the process here. Example: + + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + '', checkIfExists: true), + ] + input[1] = [ + [ id: 'alt_codon_usage' ], + [] + ] + input[2] = [ + [ id: 'allele_preference' ], + [] + ] + input[3] = "human" + """ + } + } + + then { + assert process.success + assertAll( + { assert snapshot( + process.out, + process.out.findAll { key, val -> key.startsWith('versions') } + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap new file mode 100644 index 000000000000..b7e64383bd41 --- /dev/null +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap @@ -0,0 +1,144 @@ +{ + "sarscov2 - tsv": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" + ] + ], + "1": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ], + "2": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "thimble": [ + [ + { + "id": "test" + }, + "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" + ] + ], + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + }, + { + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + } + ], + "timestamp": "2026-03-13T09:44:49.452947874", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, + "sarscov2 - tsv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ], + "2": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "thimble": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + }, + { + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + } + ], + "timestamp": "2026-03-13T09:44:53.617424268", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + } +} \ No newline at end of file From 32c725666065415e0210b3026a6a8f8ff6161ccd Mon Sep 17 00:00:00 2001 From: Clara0611 Date: Fri, 13 Mar 2026 11:28:32 +0100 Subject: [PATCH 2/5] added testdata for stitchr --- modules/nf-core/stitchr/thimble/tests/main.nf.test | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test b/modules/nf-core/stitchr/thimble/tests/main.nf.test index 53e0d755f495..0ef392f0aa7f 100644 --- a/modules/nf-core/stitchr/thimble/tests/main.nf.test +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + '', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true), ] input[1] = [ [ id: 'alt_codon_usage' ], @@ -56,7 +56,7 @@ nextflow_process { input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + '', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true), ] input[1] = [ [ id: 'alt_codon_usage' ], From 24a0f8437609567aa65cffb74c7e0263d993d3a2 Mon Sep 17 00:00:00 2001 From: Clara0611 Date: Fri, 20 Mar 2026 13:05:50 +0100 Subject: [PATCH 3/5] stitchr meta.yaml fix --- modules/nf-core/stitchr/thimble/meta.yml | 65 ++++---- .../stitchr/thimble/tests/main.nf.test | 4 - .../stitchr/thimble/tests/main.nf.test.snap | 142 ++++++++++++++++++ 3 files changed, 181 insertions(+), 30 deletions(-) diff --git a/modules/nf-core/stitchr/thimble/meta.yml b/modules/nf-core/stitchr/thimble/meta.yml index 8e1d7b385e8e..a5e3d006e9e9 100644 --- a/modules/nf-core/stitchr/thimble/meta.yml +++ b/modules/nf-core/stitchr/thimble/meta.yml @@ -1,18 +1,20 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "stitchr_thimble" -description: Automatic TCR nucleotide sequence generation from V, J and CDR3 information +description: Automatic TCR nucleotide sequence generation from V, J and CDR3 + information keywords: - TCR - sequence - immunology tools: - "stitchr": - description: "Automatic TCR nucleotide sequence generation from V, J and CDR3 information" + description: "Automatic TCR nucleotide sequence generation from V, J and CDR3 + information" homepage: "https://github.com/JamieHeather/stitchr" documentation: "https://jamieheather.github.io/stitchr/index.html" tool_dev_url: "https://github.com/JamieHeather/stitchr" doi: "10.1093/nar/gkac190" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - "imgtgenedl": description: "provides access to TCR and IG genes stored in IMGT/GENE-DB" @@ -20,34 +22,43 @@ tools: documentation: "https://github.com/JamieHeather/IMGTgeneDL/blob/main/README.md" tool_dev_url: "https://github.com/JamieHeather/IMGTgeneDL" doi: "10.1093/nar/gkab1136" - licence: ["MIT"] + licence: + - "MIT" identifier: "" - input: - - meta: type: map description: | - Groovy Map containing sample information + Groovy Map containing per sample information e.g. `[ id:'sample1' ]` - samplesheet: type: file description: tsv containing J,V and CDR3 information pattern: "*.tsv" - ontologies: [] + ontologies: + - edam: http://edamontology.org/format_3475 + - - meta2: + type: map + description: | + Information about codon usage - alt_codon_usage: type: file description: txt containing alternative codon usage in kazusa-like format pattern: "*.txt" ontologies: [] + - - meta3: + type: map + description: | + Information about non-standard allele preferences - allele_preferences: type: file description: tsv containing alternative allele preferences pattern: "*.tsv" - ontologies: [] - - species: - type: string - description: Species ("mouse" or "human") - + ontologies: + - edam: http://edamontology.org/format_3475 + - species: + type: string + description: Species ("mouse" or "human") output: thimble: - - meta: @@ -55,32 +66,31 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1' ]` - - "*.tsv": + - ${meta.id}.tsv: type: file - description: tsv containing TCR sequence information - pattern: "*.tsv" + description: | + tsv containing full TCR sequences ontologies: [] versions_stitchr: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "stitchr": + - stitchr: type: string description: The name of the tool - - "stitchr --version": + - stitchr --version: type: eval description: The expression to obtain the version of the tool versions_imgtgenedl: - - - "${task.process}": + - - ${task.process}: type: string description: The name of the process - - "imgtgenedl": + - imgtgenedl: type: string description: The name of the tool - - "imgtgenedl --version": - type: eval + - 0.6.1: + type: string description: The expression to obtain the version of the tool - topics: versions: - - ${task.process}: @@ -92,11 +102,14 @@ topics: - stitchr --version: type: eval description: The expression to obtain the version of the tool + - - ${task.process}: + type: string + description: The name of the process - imgtgenedl: type: string description: The name of the tool - - imgtgenedl --version: - type: eval + - 0.6.1: + type: string description: The expression to obtain the version of the tool authors: - "@Clara0611" diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test b/modules/nf-core/stitchr/thimble/tests/main.nf.test index 0ef392f0aa7f..8a31e353ce76 100644 --- a/modules/nf-core/stitchr/thimble/tests/main.nf.test +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test @@ -14,8 +14,6 @@ nextflow_process { when { process { """ - // TODO nf-core: define inputs of the process here. Example: - input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true), @@ -52,8 +50,6 @@ nextflow_process { when { process { """ - // TODO nf-core: define inputs of the process here. Example: - input[0] = [ [ id:'test' ], file(params.modules_testdata_base_path + 'genomics/homo_sapiens/stitchr/stitchr_vdjdb.tsv', checkIfExists: true), diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap index b7e64383bd41..5c966783767a 100644 --- a/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap @@ -1,4 +1,75 @@ { + "human - tsv": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" + ] + ], + "1": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ], + "2": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "thimble": [ + [ + { + "id": "test" + }, + "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" + ] + ], + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + }, + { + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + } + ], + "timestamp": "2026-03-13T11:30:47.61680281", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } + }, "sarscov2 - tsv": { "content": [ { @@ -140,5 +211,76 @@ "nf-test": "0.9.4", "nextflow": "25.10.4" } + }, + "human - tsv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ], + "2": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "thimble": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + }, + { + "versions_imgtgenedl": [ + [ + "STITCHR_THIMBLE", + "imgtgenedl", + "0.6.1" + ] + ], + "versions_stitchr": [ + [ + "STITCHR_THIMBLE", + "stitchr", + "1.3.1" + ] + ] + } + ], + "timestamp": "2026-03-13T11:30:52.259782431", + "meta": { + "nf-test": "0.9.4", + "nextflow": "25.10.4" + } } } \ No newline at end of file From 8e6f619b3b41a8ce494b4aeb031c6fdbaa931288 Mon Sep 17 00:00:00 2001 From: Clara0611 Date: Fri, 20 Mar 2026 14:03:34 +0100 Subject: [PATCH 4/5] new snapshot --- .../stitchr/thimble/tests/main.nf.test.snap | 146 +----------------- 1 file changed, 2 insertions(+), 144 deletions(-) diff --git a/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap index 5c966783767a..97a42c2b1c43 100644 --- a/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap +++ b/modules/nf-core/stitchr/thimble/tests/main.nf.test.snap @@ -64,149 +64,7 @@ ] } ], - "timestamp": "2026-03-13T11:30:47.61680281", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "sarscov2 - tsv": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" - ] - ], - "1": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ], - "2": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "thimble": [ - [ - { - "id": "test" - }, - "test.tsv:md5,1dc2864a6189891ae9e6bc4d4b377897" - ] - ], - "versions_imgtgenedl": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "versions_stitchr": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ] - }, - { - "versions_imgtgenedl": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "versions_stitchr": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ] - } - ], - "timestamp": "2026-03-13T09:44:49.452947874", - "meta": { - "nf-test": "0.9.4", - "nextflow": "25.10.4" - } - }, - "sarscov2 - tsv - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ], - "2": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "thimble": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions_imgtgenedl": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "versions_stitchr": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ] - }, - { - "versions_imgtgenedl": [ - [ - "STITCHR_THIMBLE", - "imgtgenedl", - "0.6.1" - ] - ], - "versions_stitchr": [ - [ - "STITCHR_THIMBLE", - "stitchr", - "1.3.1" - ] - ] - } - ], - "timestamp": "2026-03-13T09:44:53.617424268", + "timestamp": "2026-03-20T14:02:23.190588215", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" @@ -277,7 +135,7 @@ ] } ], - "timestamp": "2026-03-13T11:30:52.259782431", + "timestamp": "2026-03-20T14:02:45.410312976", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" From 5f596487450fe6518630d0c38cd55b80222c01e1 Mon Sep 17 00:00:00 2001 From: Clara0611 Date: Mon, 23 Mar 2026 13:41:09 +0100 Subject: [PATCH 5/5] pre-commit prettier changes to environment.yml --- modules/nf-core/stitchr/thimble/environment.yml | 10 ++++++++++ modules/nf-core/stitchr/thimble/main.nf | 1 + 2 files changed, 11 insertions(+) create mode 100644 modules/nf-core/stitchr/thimble/environment.yml diff --git a/modules/nf-core/stitchr/thimble/environment.yml b/modules/nf-core/stitchr/thimble/environment.yml new file mode 100644 index 000000000000..70ea7de4a894 --- /dev/null +++ b/modules/nf-core/stitchr/thimble/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - conda-forge::pip=26.0.1 + - conda-forge::python=3.14.3 + - pip: + - stitchr==1.3.1 diff --git a/modules/nf-core/stitchr/thimble/main.nf b/modules/nf-core/stitchr/thimble/main.nf index 158c0a6df34a..d80ded1b4c8b 100644 --- a/modules/nf-core/stitchr/thimble/main.nf +++ b/modules/nf-core/stitchr/thimble/main.nf @@ -3,6 +3,7 @@ process STITCHR_THIMBLE { label 'process_single' + conda "${moduleDir}/environment.yml" container "ghcr.io/qbic-pipelines/stitchr:1.3.1"