From c7b73a86046d8f05a8c082a346c1d6dda34f8643 Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Thu, 14 Nov 2024 14:58:42 +0100 Subject: [PATCH 01/16] update malt/build module --- modules/nf-core/malt/build/environment.yml | 2 +- modules/nf-core/malt/build/main.nf | 8 ++++---- modules/nf-core/malt/build/meta.yml | 10 ++++++---- modules/nf-core/malt/build/tests/main.nf.test | 4 ++-- 4 files changed, 13 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/malt/build/environment.yml b/modules/nf-core/malt/build/environment.yml index 15a775008fc..2e3a66a93e3 100644 --- a/modules/nf-core/malt/build/environment.yml +++ b/modules/nf-core/malt/build/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::malt=0.61 + - bioconda::malt=0.62 diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 6f05e9edcef..42af23b0811 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -4,11 +4,11 @@ process MALT_BUILD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/malt:0.61--hdfd78af_0' : - 'biocontainers/malt:0.61--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/malt:0.62--hdfd78af_0' : + 'biocontainers/malt:0.62--hdfd78af_0' }" input: - path fastas + path fastas_dir path gff path mapping_db @@ -27,7 +27,7 @@ process MALT_BUILD { """ malt-build \\ -v \\ - --input ${fastas.join(' ')} \\ + --input $fastas_dir \\ $igff \\ -d 'malt_index/' \\ -t $task.cpus \\ diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml index da1fc6c260d..5818a2e3d6b 100644 --- a/modules/nf-core/malt/build/meta.yml +++ b/modules/nf-core/malt/build/meta.yml @@ -21,10 +21,10 @@ tools: licence: ["GPL v3"] identifier: "" input: - - - fastas: - type: file - description: Directory of, or list of FASTA reference files for indexing - pattern: "*/|*.fasta" + - - fastas_dir: + type: directory + description: Directory of a list of FASTA reference files for indexing + pattern: "*/" - - gff: type: file description: Directory of, or GFF3 files of input FASTA files @@ -51,5 +51,7 @@ output: pattern: "malt-build.log" authors: - "@jfy133" + - "@LilyAnderssonLee" maintainers: - "@jfy133" + - "@LilyAnderssonLee" diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index 229460271c6..3b66cf979bb 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -27,7 +27,7 @@ nextflow_process { when { process { """ - input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + "genomics/prokaryotes/metagenome/fasta/", checkIfExists: true) input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } """ @@ -65,7 +65,7 @@ nextflow_process { when { process { """ - input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + "genomics/prokaryotes/metagenome/fasta/", checkIfExists: true) input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } """ From d0100b888b4b7c24671add868096920ed9ca609c Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Fri, 15 Nov 2024 13:25:44 +0100 Subject: [PATCH 02/16] use stageAs for input fasta files --- modules/nf-core/malt/build/main.nf | 4 ++-- modules/nf-core/malt/build/meta.yml | 8 +++---- modules/nf-core/malt/build/tests/main.nf.test | 10 ++++++-- .../malt/build/tests/main.nf.test.snap | 24 +++++++++---------- 4 files changed, 26 insertions(+), 20 deletions(-) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index 42af23b0811..faf6080832a 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -8,7 +8,7 @@ process MALT_BUILD { 'biocontainers/malt:0.62--hdfd78af_0' }" input: - path fastas_dir + path(fastas, stageAs: 'fa_folder/') path gff path mapping_db @@ -27,7 +27,7 @@ process MALT_BUILD { """ malt-build \\ -v \\ - --input $fastas_dir \\ + --input fa_folder \\ $igff \\ -d 'malt_index/' \\ -t $task.cpus \\ diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml index 5818a2e3d6b..099030a4943 100644 --- a/modules/nf-core/malt/build/meta.yml +++ b/modules/nf-core/malt/build/meta.yml @@ -21,10 +21,10 @@ tools: licence: ["GPL v3"] identifier: "" input: - - - fastas_dir: - type: directory - description: Directory of a list of FASTA reference files for indexing - pattern: "*/" + - - fastas: + type: file + description: Directory of, or list of FASTA reference files for indexing + pattern: "*/|*.fasta" - - gff: type: file description: Directory of, or GFF3 files of input FASTA files diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index 3b66cf979bb..5982c76fe2f 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -27,7 +27,10 @@ nextflow_process { when { process { """ - input[0] = file(params.modules_testdata_base_path + "genomics/prokaryotes/metagenome/fasta/", checkIfExists: true) + def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true ) + def genome_2 = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true ) + + input[0] = [genome_1,genome_2] input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } """ @@ -65,7 +68,10 @@ nextflow_process { when { process { """ - input[0] = file(params.modules_testdata_base_path + "genomics/prokaryotes/metagenome/fasta/", checkIfExists: true) + def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true ) + def genome_2 = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true ) + + input[0] = [genome_1,genome_2] input[1] = [] input[2] = UNZIP.out.unzipped_archive.map { it[1] } """ diff --git a/modules/nf-core/malt/build/tests/main.nf.test.snap b/modules/nf-core/malt/build/tests/main.nf.test.snap index 421a154d2bc..9ff080c8d32 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test.snap +++ b/modules/nf-core/malt/build/tests/main.nf.test.snap @@ -8,7 +8,7 @@ ] ], "1": [ - "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97" + "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" ], "2": [ "malt-build.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -22,33 +22,33 @@ "malt-build.log:md5,d41d8cd98f00b204e9800998ecf8427e" ], "versions": [ - "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97" + "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.0" }, - "timestamp": "2024-01-26T11:49:19.685017271" + "timestamp": "2024-11-15T12:14:24.942518" }, "sarscov2 - fastq": { "content": [ - "index0.idx:md5,1954f2c00b418d00112829b0a6adb8ce", - "ref.db:md5,772a09aeb162515485b037604399f2bd", - "ref.idx:md5,7dea362b3fac8e00956a4952a3d4f474", - "ref.inf:md5,b146842067cf278ef1d23e6c2e7c0c35", - "taxonomy.idx:md5,bb335e7c378a5bd85761b6eeed16d984", + "index0.idx:md5,0ba3d8bfb7ef28d08e2a005dd3405c55", + "ref.db:md5,6b36ae031c49feaae50f4cea07d9c7f4", + "ref.idx:md5,8ba66cdf65181c7efee1d366574cb9d7", + "ref.inf:md5,042712533a0187b6566db67c6503a71e", + "taxonomy.idx:md5,e7ce35e6238f39fa0c236fcf991546e4", "taxonomy.map:md5,5bb3f2192e925bca2e61e4b54f1671e0", "taxonomy.tre:md5,f76fb2d5aa9b0d637234d48175841e0e", [ - "versions.yml:md5,52c299d59c90219b9b442ee54f1acc97" + "versions.yml:md5,4ad582e415ed27dd4a275a149209961b" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.0" }, - "timestamp": "2024-06-30T19:04:45.72181253" + "timestamp": "2024-11-15T12:13:59.078459" } } \ No newline at end of file From 3a2cc81f4243be767bb1585ac122f7dccdf6449a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 21 Nov 2024 15:16:17 +0100 Subject: [PATCH 03/16] Try HTTPS rather than s3 --- modules/nf-core/malt/build/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index 5982c76fe2f..ec4ed8a53bf 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { script "../../../unzip/main.nf" process { """ - input[0] = [[], file("s3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] + input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] """ } } From f5cdb8cd9cece04b7b7e7af4e6e03413808b50af Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 09:01:05 +0000 Subject: [PATCH 04/16] Trying manually restricting memory --- modules/nf-core/malt/build/main.nf | 20 +++++++++---------- modules/nf-core/malt/build/tests/main.nf.test | 3 +++ .../nf-core/malt/build/tests/nextflow.config | 5 +---- 3 files changed, 13 insertions(+), 15 deletions(-) diff --git a/modules/nf-core/malt/build/main.nf b/modules/nf-core/malt/build/main.nf index faf6080832a..b0f22492287 100644 --- a/modules/nf-core/malt/build/main.nf +++ b/modules/nf-core/malt/build/main.nf @@ -1,20 +1,18 @@ process MALT_BUILD { - label 'process_high' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/malt:0.62--hdfd78af_0' : - 'biocontainers/malt:0.62--hdfd78af_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/malt:0.62--hdfd78af_0' + : 'biocontainers/malt:0.62--hdfd78af_0'}" input: - path(fastas, stageAs: 'fa_folder/') + path fastas, stageAs: 'fa_folder/' path gff path mapping_db output: - path "malt_index/" , emit: index - path "versions.yml" , emit: versions + path "malt_index/", emit: index + path "versions.yml", emit: versions path "malt-build.log", emit: log when: @@ -26,12 +24,12 @@ process MALT_BUILD { """ malt-build \\ + ${args} \\ -v \\ --input fa_folder \\ - $igff \\ + ${igff} \\ -d 'malt_index/' \\ - -t $task.cpus \\ - $args \\ + -t ${task.cpus} \\ -mdb ${mapping_db}/*.db |&tee malt-build.log cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index ec4ed8a53bf..a49787b9d3a 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -25,6 +25,9 @@ nextflow_process { test("sarscov2 - fastq") { when { + params { + module_args = '-J-Xmx6G --sequenceType DNA' + } process { """ def genome_1 = file(params.modules_testdata_base_path + 'genomics/prokaryotes/metagenome/fasta/sarscov2.fasta', checkIfExists: true ) diff --git a/modules/nf-core/malt/build/tests/nextflow.config b/modules/nf-core/malt/build/tests/nextflow.config index c538bb5b9d8..f1c7169581e 100644 --- a/modules/nf-core/malt/build/tests/nextflow.config +++ b/modules/nf-core/malt/build/tests/nextflow.config @@ -1,8 +1,5 @@ process { - - withName: MALT_BUILD { - ext.args = "--sequenceType DNA" + ext.args = params.module_args } - } From 2d2273afe6cb24b2742ce82d9d9cb2d6c697c02f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 10:48:14 +0100 Subject: [PATCH 05/16] Move config loading to the right place --- modules/nf-core/malt/build/tests/main.nf.test | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index a49787b9d3a..80252eb3bc0 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process MALT_BUILD" script "../main.nf" process "MALT_BUILD" - config "./nextflow.config" tag "modules" tag "modules_nfcore" @@ -23,7 +22,7 @@ nextflow_process { } test("sarscov2 - fastq") { - + config "./nextflow.config" when { params { module_args = '-J-Xmx6G --sequenceType DNA' @@ -65,7 +64,7 @@ nextflow_process { } test("sarscov2 - fastq - stub") { - + config "./nextflow.config" options "-stub" when { From 15a1f23c4606a171a766eeb5f7c334b240f3fdbb Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 20:11:16 +0100 Subject: [PATCH 06/16] Update modules/nf-core/malt/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal --- modules/nf-core/malt/build/tests/main.nf.test | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/malt/build/tests/main.nf.test b/modules/nf-core/malt/build/tests/main.nf.test index 80252eb3bc0..a2a0db8b242 100644 --- a/modules/nf-core/malt/build/tests/main.nf.test +++ b/modules/nf-core/malt/build/tests/main.nf.test @@ -64,7 +64,6 @@ nextflow_process { } test("sarscov2 - fastq - stub") { - config "./nextflow.config" options "-stub" when { From 719c5c2765f3ca5f862461739f3ad87518351dee Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 20:21:45 +0100 Subject: [PATCH 07/16] Update main.nf.test --- modules/nf-core/malt/run/tests/main.nf.test | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test index 304c01d4a21..ad206451cc4 100644 --- a/modules/nf-core/malt/run/tests/main.nf.test +++ b/modules/nf-core/malt/run/tests/main.nf.test @@ -17,12 +17,17 @@ nextflow_process { script "../../../unzip/main.nf" process { """ - input[0] = [[], file("s3://ngi-igenomes/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] + input[0] = [[], file("https://ngi-igenomes.s3.eu-west-1.amazonaws.com/test-data/createtaxdb/taxonomy/megan-nucl-Feb2022.db.zip", checkIfExists: true)] """ } } run("MALT_BUILD") { script "../../../malt/build/main.nf" + when { + params { + module_args = '-J-Xmx6G --sequenceType DNA' + } + } process { """ input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) From 044a7d4cdbc148e99166cc772ca1fdd75fdc685d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 20:22:23 +0100 Subject: [PATCH 08/16] Update nextflow.config --- modules/nf-core/malt/run/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 34fc9b7e266..7abd15bc81a 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -7,7 +7,7 @@ process { } withName: MALT_BUILD { - ext.args = "--sequenceType DNA" + ext.args = params.module_args } } From 96f606762cfa06bfa863bbe94edcb5a5d94a6b1a Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 19:53:23 +0000 Subject: [PATCH 09/16] Get tests running --- modules/nf-core/malt/run/tests/main.nf.test | 5 ----- modules/nf-core/malt/run/tests/nextflow.config | 11 +++++------ 2 files changed, 5 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/malt/run/tests/main.nf.test b/modules/nf-core/malt/run/tests/main.nf.test index ad206451cc4..a75fe4ee49c 100644 --- a/modules/nf-core/malt/run/tests/main.nf.test +++ b/modules/nf-core/malt/run/tests/main.nf.test @@ -23,11 +23,6 @@ nextflow_process { } run("MALT_BUILD") { script "../../../malt/build/main.nf" - when { - params { - module_args = '-J-Xmx6G --sequenceType DNA' - } - } process { """ input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 7abd15bc81a..ea90179f64b 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -1,13 +1,12 @@ process { + withName: MALT_BUILD { + ext.args = "-J-Xmx6G --sequenceType DNA" + memory = 12.GB + } withName: MALT_RUN { ext.args = "-m BlastN -J-Xmx8G -a . -f SAM" - memory = 12.GB - } - - withName: MALT_BUILD { - ext.args = params.module_args + memory = 12.GB } - } From 84e0ba6067fc4d6f2d0f43ce123cf17dc98c7815 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 19:57:51 +0000 Subject: [PATCH 10/16] Adjust to VM minimum --- modules/nf-core/malt/run/tests/nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index ea90179f64b..5a0b3908bff 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -2,11 +2,11 @@ process { withName: MALT_BUILD { ext.args = "-J-Xmx6G --sequenceType DNA" - memory = 12.GB + memory = 6.GB } withName: MALT_RUN { ext.args = "-m BlastN -J-Xmx8G -a . -f SAM" - memory = 12.GB + memory = 6.GB } } From 91725cad264f37bf1a6b4f753d8025793cb70930 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 25 Nov 2024 19:58:01 +0000 Subject: [PATCH 11/16] And MALT_RUN --- modules/nf-core/malt/run/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 5a0b3908bff..e476eb87990 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -6,7 +6,7 @@ process { } withName: MALT_RUN { - ext.args = "-m BlastN -J-Xmx8G -a . -f SAM" + ext.args = "-m BlastN -J-Xmx6G -a . -f SAM" memory = 6.GB } } From b2901178a34a3260f9b7dde621d9bbe2590643f8 Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Wed, 27 Nov 2024 11:20:03 +0100 Subject: [PATCH 12/16] use process.resourceLimits defining the memory limit --- modules/nf-core/malt/run/tests/nextflow.config | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index e476eb87990..b6246497317 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -1,12 +1,16 @@ +process { + resourceLimits = [ + memory: '6.GB' + ] +} + process { withName: MALT_BUILD { ext.args = "-J-Xmx6G --sequenceType DNA" - memory = 6.GB } withName: MALT_RUN { ext.args = "-m BlastN -J-Xmx6G -a . -f SAM" - memory = 6.GB } } From ff0f85e0bc42b59a398a3dc6a9017b4905f817a4 Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Wed, 27 Nov 2024 12:38:04 +0100 Subject: [PATCH 13/16] Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal --- modules/nf-core/malt/run/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index b6246497317..4fb8d946d3c 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -7,7 +7,7 @@ process { process { withName: MALT_BUILD { - ext.args = "-J-Xmx6G --sequenceType DNA" + ext.args = { "-J-Xmx${task.memory.toGiga()}G --sequenceType DNA" } } withName: MALT_RUN { From 62e1cda06ba5111270b72018d9a51daf67749092 Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Wed, 27 Nov 2024 12:38:11 +0100 Subject: [PATCH 14/16] Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal --- modules/nf-core/malt/run/tests/nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 4fb8d946d3c..728c2ebce65 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -1,7 +1,4 @@ process { - resourceLimits = [ - memory: '6.GB' - ] } process { From bb460e419884a80e039dabecfe665c98ae884961 Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Wed, 27 Nov 2024 12:38:26 +0100 Subject: [PATCH 15/16] Update modules/nf-core/malt/run/tests/nextflow.config Co-authored-by: Mahesh Binzer-Panchal --- modules/nf-core/malt/run/tests/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 728c2ebce65..1a22d808cd3 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -8,6 +8,6 @@ process { } withName: MALT_RUN { - ext.args = "-m BlastN -J-Xmx6G -a . -f SAM" + ext.args = { "-m BlastN -J-Xmx${task.memory.toGiga()}G -a . -f SAM" } } } From d0886cec847a368e1e1041d9b8d7a3c30f139833 Mon Sep 17 00:00:00 2001 From: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Date: Wed, 27 Nov 2024 12:43:23 +0100 Subject: [PATCH 16/16] Update nextflow.config --- modules/nf-core/malt/run/tests/nextflow.config | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/nf-core/malt/run/tests/nextflow.config b/modules/nf-core/malt/run/tests/nextflow.config index 1a22d808cd3..8918381db86 100644 --- a/modules/nf-core/malt/run/tests/nextflow.config +++ b/modules/nf-core/malt/run/tests/nextflow.config @@ -1,6 +1,3 @@ -process { -} - process { withName: MALT_BUILD {